Biofuel production

ABSTRACT

Methods, enzymes, recombinant microorganism, and microbial systems are provided for converting polysaccharides, such as those derived from biomass, into suitable monosaccharides or oligosaccharides, as well as for converting suitable monosaccharides or oligosaccharides into commodity chemicals, such as biofuels. Commodity chemicals produced by the methods described herein are also provided. Commodity chemical enriched, refinery-produced petroleum products are also provided, as well as methods for producing the same.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of copending U.S. patent applicationSer. No. 12/245,537, with a filing date of Oct. 3, 2008, which claimsthe benefit under 35 U.S.C. §119(e) of U.S. Provisional PatentApplication No. 60/977,628 filed Oct. 4, 2007, all of which areincorporated herein by reference in their entirety.

SUBMISSION OF SEQUENCE LISTING AS ASCII TEXT FILE

The content of the following submission on ASCII text file isincorporated herein by reference in its entirety: a computer readableform (CRF) of the Sequence Listing (file name: 690212000604SeqList.txt,date recorded: Mar. 23, 2011, size: 519 KB).

TECHNICAL FIELD

The present application relates generally to the use of microbial andchemical systems to convert biomass to commodity chemicals, such asbiofuels/biopetrols.

BACKGROUND

Petroleum is facing declining global reserves and contributes to morethan 30% of greenhouse gas emissions driving global warming. Annually800 billion barrels of transportation fuel are consumed globally. Dieseland jet fuels account for greater than 50% of global transportationfuels.

Significant legislation has been passed, requiring fuel producers to capor reduce the carbon emissions from the production and use oftransportation fuels. Fuel producers are seeking substantially similar,low carbon fuels that can be blended and distributed through existinginfrastructure (e.g., refineries, pipelines, tankers).

Due to increasing petroleum costs and reliance on petrochemicalfeedstocks, the chemicals industry is also looking for ways to improvemargin and price stability, while reducing its environmental footprint.The chemicals industry is striving to develop greener products that aremore energy, water, and CO₂ efficient than current products. Fuelsproduced from biological sources, such as biomass, represent one aspectof process.

Presents method for converting biomass into biofuels focus on the use oflignocellulolic biomass, and there are many problems associated withusing this process. Large-scale cultivation of lignocellulolic biomassrequires substantial amount of cultivated land, which can be onlyachieved by replacing food crop production with energy crop production,deforestation, and by recultivating currently uncultivated land. Otherproblems include a decrease in water availability and quality and anincrease in the use of pesticides and fertilizers.

The degradation of lignocellulolic biomass using biological systems is avery difficult challenge due to its substantial mechanistic strength andthe complex chemical components. Approximately thirty different enzymesare required to fully convert lignocellulose to monosaccharides. Theonly available alternate to this complex approach requires a substantialamount of heat, pressure, and strong acids. The art therefore needs aneconomic and technically simple process for converting biomass intohydrocarbons for use as biofuels or biopetrols.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the Vibrio splendidus genomic region of the fosmid clonedescribed in Example 1. Genes are indicated with orange arrows. Labelsshow the numerical gene indices and the predicted function of theproteins.

FIG. 2 illustrates the pathways involved in certain embodiment in whichE. coli may be engineered to grow on alginate as a sole source ofcarbon.

FIG. 3 illustrates the pathways involved in certain embodiment in whichE. coli may be engineered to grow on pectin as a sole source of carbon.

FIG. 4 shows the results of engineered or recombinant E. coli growing onalginate as a sole source of carbon (see solid circles). Agrobacteriumtumefaciens cells provide a positive control (see hatched circles). Thewell to the immediate left of the of the A. tumefaciens positive controlcontains DH10B E. coli cells, which provide a negative control.

FIG. 5 shows the growth of recombinant strain of E. coli ongalacturonates and pectin. FIG. 5A shows the growth of E. coli onvarious lengths of galacturonate after 24 hr. The recombinant strain inFIG. 5A is the E. coli BL21(DE3) strain harboringpTrlogl-kdgR+pBBRGal3P, and the control strain is the BL21(DE3) strainharboring pTrc99A+pBBR1MCS-2, as described in Example 2. FIG. 5B showsthe growth of recombinant E. coli on pectin after 3-4 days. Therecombinant strain in FIG. 5B is E. coli DH5a strain containing pPEL74(Ctrl) and pPEL74 and pROU2, as described in Example 2.

FIG. 6 shows the degradation of alginate to form pyruvate. FIG. 6Aillustrates a simplified metabolic pathway for alginate degradation andmetabolism. FIG. 6B shows the results of in vitro degradation ofalginate to form pyruvate by an enzymatic degradation route. FIG. 6Cshows the results of in vitro degradation of alginate to form pyruvateby a chemical degradation route.

FIG. 7 shows the biological activity of various alcohol dehydrogenasesisolated from Agrobacterium tumefaciens C58. FIG. 7A shows DEHUhydrogenase activity as monitored by NADPH consumption, and FIG. 7Bshows mannuronate hydrogenase activity as monitored by NADPHconsumption.

FIG. 8 shows the GC-MS chromatogram results for the control sample (FIG.8A) and for isobutyraldehyde, 3-methylpentanol, and 2-methylpentanalproduction from pBADalsS-ilvCD-leuABCD2 and pTrcBALK (FIG. 8B).

FIG. 9 shows the GC-MS chromatogram results for the control sample (FIG.9A) and for 4-hydroxyphenylethanol and indole-3-ethanol production frompBADtyrA-aroLAC-aroG-tktA-aroBDE and pTrcBALK (FIG. 9B).

FIG. 10 shows the mass spectrometry results for isobutanal (FIG. 10A),3-methylpentanol (FIG. 10B), and 2-methylpentanol (FIG. 10C).

FIG. 11 shows the mass spectrometry results for phenylethanol (FIG.11A), 4-hydroxyphenylethanol (FIG. 11B), and indole-3-ethanol (FIG.11C).

FIG. 12 shows the biological activity of diol dehydratases. FIG. 12Ashows the reduction of butyroin by ddh1, ddh2, and ddh3 as monitored byNADH consumption. FIG. 12B shows the oxidation activity of ddh3 towards1,2-cyclopentanediol and 1,2-cyclohexanediol as measured by NADHproduction.

FIG. 13 summarizes the results of kinetic studies for various substratesin the oxidation reactions catalyzed by the DDH polypeptides. Thesereactions were NAD+dependent.

FIG. 14 shows the nucleotide sequence (FIG. 14A) (SEQ ID NO:97) andpolypeptide sequence (FIG. 14B) (SEQ ID NO:98) of diol dehydrogenaseDDH1 isolated from Lactobaccilus brevis ATCC 367.

FIG. 15 shows the nucleotide sequence (FIG. 15A) (SEQ ID NO:99) andpolypeptide sequence (FIG. 15B) (SEQ ID NO:100) of diol dehydrogenaseDDH2 isolated from Pseudomonas putida KT2440.

FIG. 16 shows the nucleotide sequence (FIG. 16A) (SEQ ID NO:101) andpolypeptide sequence (FIG. 16B) (SEQ ID NO:102) of diol dehydrogenaseDDH3 isolated from Kiebsiella pneumoniae MGH78578.

FIG. 17 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This reaction illustrates the sequential conversion of butanalinto 5-hydroxy-4-octanone and then 4,5-octanonediol. FIG. 17A shows thedetection of butyroin (5-hydroxy-4-octanone) at 5.36 minutes, and FIG.17B shows the detection of 4,5-octanediol at 6.49 and 6.65 minutes.

FIG. 18 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This Figure illustrates the sequential conversion of n-pentanalinto 6-hydroxy-5-decanone and then 5,6-decanediol. FIG. 18A shows thedetection of valeroin (6-hydroxy-5-decanone) at 8.22 minutes, and FIG.18B shows the detection of 5,6 decanediol at 9.22 and 9.35 minutes.

FIG. 19 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This Figure illustrates the sequential conversion of3-methylbutanal into 2,7-dimethyl-5-hydroxy-4-octanone and then2,7-dimethyl-4,5-octanediol. FIG. 19A shows the detection of isoveraloin(2,7-dimethyl-5-hydroxy-4-octanone) at 6.79 minutes, and FIG. 19B showsthe detection of 2,7-dimethyl-4,5-octanediol at 7.95 and 8.15 minutes.

FIG. 20 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This Figure illustrates the sequential conversion of n-hexanalinto 7-hydroxy-6-dodecanone and then 6,7-dodecanediol. FIG. 20A showsthe detection of hexanoin (7-hydroxy-6-decanone) at 10.42 minutes, andFIG. 20B shows the detection of 6,7 dodecanediol at 10.89 and 10.95minutes.

FIG. 21 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This Figure illustrates the sequential conversion of4-methylpentanal into 2,9-dimethyl-6-hydroxy-5-decanone and then2,9-dimethyl-5,6-decanediol. FIG. 21A shows the detection of isohexanoin(2,9-Dimethyl-6-hydroxy-5-decanone) at 9.45 minutes, and FIG. 21B showsthe detection of 2,9-dimethyl-5,6-decanediol at 10.38 and 10.44 minutes.

FIG. 22 shows the in vivo biological activity of a benzaldehyde lyase(bal) gene isolated from Pseudomonas fluorescens (codon usage wasoptimized for E. coli protein expression) and a ddh gene isolated fromKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (DDH3). This Figureillustrates the conversion of n-octanal into 9-hydroxy-8-hexadecanone byshowing the detection of detection of octanoin(9-hydroxy-8-hexadecanone) at 12.35 minutes.

FIG. 23 shows the in vivo biological activity of a benzaldehyde lyase(bal) gene isolated from Pseudomonas fluorescens (codon usage wasoptimized for E. coli protein expression) and a ddh gene isolated fromKlebsiella pneumoniae subsp. pneumoniae MGH 78578 (DDH3). This Figureillustrates the conversion of acetaldehyde into 3-hydroxy-2-butanone byshowing the detection of acetoin (3-hydroxy-2-butanone) at rt=0.91minutes.

FIG. 24 shows the sequential in vivo biological activity of abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) and a ddhgene isolated from Klebsiella pneumoniae subsp. pneumoniae MGH 78578(DDH3). This Figure illustrates the sequential conversion of n-propanalinto 4-hydroxy-3-hexanone and then 3,4-hexanediol. FIG. 24A shows thedetection of propioin (4-hydroxy-3-hexanone) at rt=2.62 minutes, andFIG. 24B shows the detection of 3,4-hexanediol at rt=3.79 minutes.

FIG. 25 the in vivo biological activity of a benzaldehyde lyase (bal)gene isolated from Pseudomonas fluorescens (codon usage was optimizedfor E. coli protein expression) and a ddh gene isolated from Klebsiellapneumoniae subsp. pneumoniae MGH 78578 (DDH3). This Figure illustratesthe conversion of phenylacetoaldehyde into1,4-diphenyl-3-hydroxy-2-butanone by showing the detection of1,4-diphenyl-3-hydroxy-2-butanone at rt=13.66 minutes.

FIG. 26 shows the sequential biological activity of a diol dehydrogenaseddh from Kiebsiella pneumoniae MGH 78578 (DDH3) and a diol dehydratasepduCDE from Kiebsiella pneumoniae MGH 78578. FIG. 26A shows GC-MS datawhich confirms the presence of 4,5-octanediol in the sample extraction,which is the expected product resulting from the reduction of butyroinby ddh3. FIG. 26B shows GC-MS data confirming the presence of 4-octanonein the sample extraction, which is the expected product resulting fromthe sequential dehydrogenation of butyroin and dehydration of4,5-octanediol by ddh3 and pduCDE, respectively.

FIG. 27 shows the sequential biological activity of a diol dehydrogenaseddh from Kiebsiella pneumoniae MGH 78578 (DDH3) and a diol dehydratasepduCDE from Kiebsiella pneumoniae MGH 78578. FIGS. 27A and 27B showcomparisons between the sample extraction gas chromatograph/massspectrum and the 4-octanone standard gas chromatograph/mass spectrum,confirming that 4-octanone was produced from butyroin using the enzymesdiol dehydrogenase (ddh3) and a diol dehydratase (pduCDE).

FIG. 28 shows the nucleotide sequence (FIG. 28A) (SEQ ID NO:103) andpolypeptide sequence (FIG. 28B) (SEQ ID NO:104) of a diol dehydrataselarge subunit (pduC) isolated from Klebsiella pneumoniae MGH78578.

FIG. 29 shows the nucleotide sequence (FIG. 29A) (SEQ ID NO:105) andpolypeptide sequence (FIG. 29B) (SEQ ID NO:106) of a diol dehydratasemedium subunit isolated from Klebsiella pneumoniae MGH78578 (pduD), inaddition to the nucleotide sequence (FIG. 29C) (SEQ ID NO:107) andpolypeptide sequence (FIG. 29D) (SEQ ID NO:108) of a diol dehydratasesmall subunit isolated from Klebsiella pneumoniae MGH78578 (pduE).

FIG. 30 shows the oxidation of 4-octanol by secondary alcoholdehydrogenases as monitored by NADH production (FIG. 30A) and NADPHproduction (FIG. 30B).

FIG. 31 shows the oxidation of 4-octanol by secondary alcoholdehydrogenases as monitored by NADH production (FIG. 31A) and NADPHproduction (FIG. 31B).

FIG. 32 shows the oxidation of 2,7-dimethyl octanol by secondary alcoholdehydrogenases as monitored by NADH production (FIG. 32A) and NADPHproduction (FIG. 32B).

FIG. 33 shows the oxidation and reduction activity of 2ADH11 and 2ADH16.FIG. 33A shows the reduction of 2,7-dimethyl-4-octanone as measured byNADPH consumption. FIG. 33B shows the reduction of2,7-dimethyl-4-octanone, 4-octanone, and cyclolypentanone.

FIG. 34 shows the oxidation and reduction of cyclopentanol by secondaryalcohol dehydrogenases. FIG. 34A shows the oxidation of cyclopentanol asmonitored by NADH or NADPH formation. FIG. 34B shows the reduction ofcyclopentanol as monitored by NADPH consumption.

FIG. 35 shows the calculated rate constants for the illustratedreduction reactions for each substrate catalyzed by secondary alcoholdehydrogenase ADH-16 (SEQ ID NO:138).

FIG. 36 shows the calculated rate constants for the illustratedoxidation reactions for each substrate catalyzed by secondary alcoholdehydrogenase ADH-16 (SEQ ID NO:138).

FIG. 37 shows a list of alginate lyases genes/proteins that may beutilized according to the methods and recombinant microorganismsdescribed herein.

FIG. 38 shows a list of pectate lyase genes/proteins that may beutilized according to the methods and recombinant microorganismsdescribed herein.

FIG. 39A shows a list of rhamnogalacturonan lyase genes/proteins thatmay be utilized according to the methods and recombinant microorganismsdescribed herein. FIG. 39B shows a list of rhamnogalacturonate hydrolasegenes/proteins that may be utilized according to the methods andrecombinant microorganisms described herein.

FIG. 40 shows a list of pectin methyl esterase genes/proteins that maybe utilized according to the methods and recombinant microorganismsdescribed herein.

FIG. 41 shows a list of pectin acetyl esterase genes/proteins that maybe utilized according to the methods and recombinant microorganismsdescribed herein.

FIG. 42 shows the production of 2-phenyl ethanol (FIG. 42A),2-(4-hydroxyphenyl)ethanol (FIG. 42B), and 2-(indole-3-)ethanol (FIG.42C) at 24 hours from the recombinant microorganisms described inExample 4, which comprise functional 2-phenylethanol,2-(4-hydroxyphenyl)ethanol, and 2-(indole-3-)ethanol biosynthesispathways.

FIG. 43 shows the GC-MS chromatogram results that confirm the productionof 2-phenyl ethanol (FIG. 43B) at one week from the recombinantmicroorganisms described in Example 4 (pBADpheA-aroLAC-aroG-tktA-aroBDEand pTrcBALK). FIG. 43A shows the negative control cells (pBAD33 andpTrc99A).

FIG. 44 shows the GC-MS chromatogram results that confirm the productionof 2-(4-hydroxyphenyl)ethanol (9.36 min) and 2-(indole-3) ethanol (10.32min) at one week from the recombinant microorganisms described inExample 4 (pBADtyrA-aroLAC-aroG-tktA-aroBDE and pTrcBALK).

FIG. 45 confirms both the formation of 1-propanal from 1,2-propanediol(FIG. 45A), and the formation of 2-butanone from meso-2,3-butanediol(FIG. 45B), both of which were catalyzed in vitro by an isolated B12independent diol dehydratase, as described in Example 9.

FIG. 46A shows the in vivo production of 1-propanol from1,2-propanediol. FIG. 46B shows the in vivo production of 2-butanol frommeso-2,3 butanediol. FIG. 46C shows the in vivo production ofcyclopentanone from trans-1,2-cyclopentanediol. These experiments wereperformed as described in Example 9.

FIG. 47 shows the results of the TBA assay, as performed in Example 10.The left tube in FIG. 47 represents media taken from an overnightculture of cells expressing Vs24254, showing secretion of an alginatelyase, while the right hand tube shows the TBA reaction using media fromcells expressing Vs24259 (negative control). The lack of pink colorationin the negative control indicates that little or no cleavage of thealginate polymer has occurred.

FIG. 48 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized benzaldehyde lyase (BAL)catalyzed the in vivo production of 3-hydroxy-2-pentanone and2-hydroxy-3-pentanone from a ligation reaction between acetaldehyde andpropionaldehyde (FIG. 48A), and catalyzed the in vivo production of4-hydroxy-3-heptanone and 3-hydroxy-4-heptanone from a ligation reactionbetween propionaldehyde and butyraldehyde (FIG. 48B).

FIG. 49 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 3-hydroxy-2-heptanone from a ligation reaction betweenacetaldehyde and pentanal (FIG. 49A), and catalyzed the in vivoproduction of 4-hydroxy-3-octanone and 3-hydroxy-4-octanone from aligation reaction between pentanal and propionaldehyde (FIG. 49B).

FIG. 50 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 5-hydroxy-4-nonanone from ligation reaction betweenbutyraldehyde and pentanal (FIG. 50A), and catalyzed the in vivoproduction of 2-methyl-5-hydroxy-4-decanone and2-methyl-4-hydroxy-5-decanone from ligation reaction between hexanal and3-methylbutyraldehyde (FIG. 50B).

FIG. 51 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 6-methyl-3-hydroxy-2-heptanone from ligation reactionbetween acetaldehyde and 4-methylhexanal (FIG. 51A), and catalyzed thein vivo production of 7-methyl-4-hydroxy-3-octanone from a ligationreaction between 4-methylhexanal and propionaldehyde (FIG. 51B).

FIG. 52 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 8-methyl-5-hydroxy-4-nonanone from ligation reactionbetween 4-methylhexanal and butyraldehyde (FIG. 52A), and catalyzed thein vivo production of 3-hydroxy-2-decanone from a ligation reactionbetween acetaldehyde and octanal (FIG. 52B).

FIG. 53 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 4-hydroxy-3-undecanone from ligation reaction betweenoctanal and propionaldehyde (FIG. 53A), and catalyzed the in vivoproduction of 5-hydroxy-4-dodecanone from a ligation reaction betweenoctanal and butyraldehyde (FIG. 53B).

FIG. 54 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 6-hydroxy-5-tridecanone (FIG. 54A) from ligation reactionbetween octanal and pentanal, and catalyzed the in vivo production of2-methyl-5-hydroxy-4-dodecanone and 2-methyl-4-hydroxy-5-decanone from aligation reaction between octanal and 3-methylbutyraldehyde (FIG. 54B).

FIG. 55 shows the in vivo biological activity of a C—C ligase isolatedfrom Pseudomonas fluorescens and cloned into E. coli. The GC-MSchromatogram results show that codon-optimized BAL catalyzed the in vivoproduction of 2-methyl-6-hydroxy-5-tridecanone from a ligation reactionbetween octanal and 4-methylpentanal.

FIG. 56 shows the growth of recombinant E. coli on alginate as a solesource of carbon (FIG. 56A), as described in Example 10. Growth onglucose (FIG. 56B) provides a positive control. The cells weretransformed with either no plasmid (BL21—negative control), one plasmid(e.g., Da or 3a), or two plasmids (e.g., Dk3a and Da3k). The plasmidsare indicated by the lower case letter: “a” refers to the pET-DEST42plasmid backbone and “k” refers to the pENTR/D/TOPO backbone. “D”indicates that the plasmid contains the genomic region Vs24214-24249,while “3” indicates that the plasmid contains the genomic regionVs24189-24209. Thus, Da would be pET-DEST42-Vs24214-24249, Da3k would bepET-DEST42-Vs24214-24249 and pENTR/D/TOPO-Vs24189-24209 and so on. Theseresults show that the combined genomic regions Vs24214-24249 andVs24189-24209 are sufficient to confer on E. coli the ability to grow onalginate as a sole source of carbon.

FIG. 57 shows the production of ethanol by E. coli growing on alginate,as performed in Example 11. E. coli was transformed with eitherpBBRPdc-AdhA/B or pBBRPdc-AdhA/B+1.5 FOS and allowed to grow in m9 mediacontaining alginate.

BRIEF SUMMARY

Embodiments of the present invention include methods for converting apolysaccharide to a commodity chemical, comprising (a) contacting thepolysaccharide, wherein the polysaccharide is optionally derived frombiomass, with a polysaccharide degrading or depolymerizing metabolicsystem, wherein the metabolic system is selected from; (i) enzymatic orchemical catalysis, and (ii) a microbial system, wherein the microbialsystem comprises a recombinant microorganism, wherein the recombinantmicroorganism comprises one or exogenous genes that allow it to grow onthe polysaccharide as a sole source of carbon, thereby converting thepolysaccharide to a suitable monosaccharide or oligosaccharide; and (b)contacting the suitable monosaccharide or oligosaccharide with commoditychemical biosynthesis pathway, wherein the commodity chemicalbiosynthesis pathway comprises an aldehyde or ketone biosynthesispathway, thereby converting the polysaccharide to the commoditychemical.

In certain aspects, the biomass is selected from marine biomass andvegetable/fruit/plant biomass. In certain aspects, the marine biomass isselected from kelp, giant kelp, sargasso, seaweed, algae, marinemicroflora, microalgae, and sea grass. In certain aspects, thevegetable/fruit/plant biomass comprises plant peel or pomace. In certainaspects, the vegetable/fruit/plant biomass is selected from citrus,potato, tomato, grape, gooseberry, carrot, mango, sugar-beet, apple,switchgrass, wood, and stover.

In certain aspects, the polysaccharide is selected from alginate, agar,carrageenan, fucoidan, pectin, polygalacturonate, cellulose,hemicellulose, xylan, arabinan, and mannan. In certain aspects, thesuitable monosaccharide or oligosaccharide is selected from2-keto-3-deoxy D-gluconate (KDG), D-mannitol, guluronate, mannuronate,mannitol, lyxose, glycerol, xylitol, glucose, mannose, galactose,xylose, arabinose, glucuronate, galacturonates, and rhamnose.

In certain aspects, the commodity chemical is selected from methane,methanol, ethane, ethene, ethanol, n-propane, 1-propene, 1-propanol,propanal, acetone, propionate, n-butane, 1-butene, 1-butanol, butanal,butanoate, isobutanal, isobutanol, 2-methylbutanal, 2-methylbutanol,3-methylbutanal, 3-methylbutanol, 2-butene, 2-butanol, 2-butanone,2,3-butanediol, 3-hydroxy-2-butanone, 2,3-butanedione, ethylbenzene,ethenylbenzene, 2-phenylethanol, phenylacetaldehyde, 1-phenylbutane,4-phenyl-1-butene, 4-phenyl-2-butene, 1-phenyl-2-butene,1-phenyl-2-butanol, 4-phenyl-2-butanol, 1-phenyl-2-butanone,4-phenyl-2-butanone, 1-phenyl-2,3-butandiol,1-phenyl-3-hydroxy-2-butanone, 4-phenyl-3-hydroxy-2-butanone,1-phenyl-2,3-butanedione, n-pentane, ethylphenol, ethenylphenol,2-(4-hydroxyphenyl)ethanol, 4-hydroxyphenylacetaldehyde,1-(4-hydroxyphenyl) butane, 4-(4-hydroxyphenyl)-1-butene,4-(4-hydroxyphenyl)-2-butene, 1-(4-hydroxyphenyl)-1-butene,1-(4-hydroxyphenyl)-2-butanol, 4-(4-hydroxyphenyl)-2-butanol,1-(4-hydroxyphenyl)-2-butanone, 4-(4-hydroxyphenyl)-2-butanone,1-(4-hydroxyphenyl)-2,3-butandiol,1-(4-hydroxyphenyl)-3-hydroxy-2-butanone,4-(4-hydroxyphenyl)-3-hydroxy-2-butanone,1-(4-hydroxyphenyl)-2,3-butanonedione, indolylethane, indolylethene,2-(indole-3-)ethanol, n-pentane, 1-pentene, 1-pentanol, pentanal,pentanoate, 2-pentene, 2-pentanol, 3-pentanol, 2-pentanone, 3-pentanone,4-methylpentanal, 4-methylpentanol, 2,3-pentanediol,2-hydroxy-3-pentanone, 3-hydroxy-2-pentanone, 2,3-pentanedione,2-methylpentane, 4-methyl-1-pentene, 4-methyl-2-pentene,4-methyl-3-pentene, 4-methyl-2-pentanol, 2-methyl-3-pentanol,4-methyl-2-pentanone, 2-methyl-3-pentanone, 4-methyl-2,3-pentanediol,4-methyl-2-hydroxy-3-pentanone, 4-methyl-3-hydroxy-2-pentanone,4-methyl-2,3-pentanedione, 1-phenylpentane, 1-phenyl-1-pentene,1-phenyl-2-pentene, 1-phenyl-3-pentene, 1-phenyl-2-pentanol,1-phenyl-3-pentanol, 1-phenyl-2-pentanone, 1-phenyl-3-pentanone,1-phenyl-2,3-pentanediol, 1-phenyl-2-hydroxy-3-pentanone,1-phenyl-3-hydroxy-2-pentanone, 1-phenyl-2,3-pentanedione,4-methyl-1-phenylpentane, 4-methyl-1-phenyl-1-pentene,4-methyl-1-phenyl-2-pentene, 4-methyl-1-phenyl-3-pentene,4-methyl-1-phenyl-3-pentanol, 4-methyl-1-phenyl-2-pentanol,4-methyl-1-phenyl-3-pentanone, 4-methyl-1-phenyl-2-pentanone,4-methyl-1-phenyl-2,3-pentanediol, 4-methyl-1-phenyl-2,3-pentanedione,4-methyl-1-phenyl-3-hydroxy-2-pentanone,4-methyl-1-phenyl-2-hydroxy-3-pentanone, 1-(4-hydroxyphenyl) pentane,1-(4-hydroxyphenyl)-1-pentene, 1-(4-hydroxyphenyl)-2-pentene,1-(4-hydroxyphenyl)-3-pentene, 1-(4-hydroxyphenyl)-2-pentanol,1-(4-hydroxyphenyl)-3-pentanol, 1-(4-hydroxyphenyl)-2-pentanone,1-(4-hydroxyphenyl)-3-pentanone, 1-(4-hydroxyphenyl)-2,3-pentanediol,1-(4-hydroxyphenyl)-2-hydroxy-3-pentanone,1-(4-hydroxyphenyl)-3-hydroxy-2-pentanone,1-(4-hydroxyphenyl)-2,3-pentanedione, 4-methyl-1-(4-hydroxyphenyl)pentane, 4-methyl-1-(4-hydroxyphenyl)-2-pentene,4-methyl-1-(4-hydroxyphenyl)-3-pentene,4-methyl-1-(4-hydroxyphenyl)-1-pentene,4-methyl-1-(4-hydroxyphenyl)-3-pentanol,4-methyl-1-(4-hydroxyphenyl)-2-pentanol,4-methyl-1-(4-hydroxyphenyl)-3-pentanone,4-methyl-1-(4-hydroxyphenyl)-2-pentanone,4-methyl-1-(4-hydroxyphenyl)-2,3-pentanediol,4-methyl-1-(4-hydroxyphenyl)-2,3-pentanedione,4-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-pentanone,4-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-pentanone, 1-indole-3-pentane,1-(indole-3)-1-pentene, 1-(indole-3)-2-pentene, 1-(indole-3)-3-pentene,1-(indole-3)-2-pentanol, 1-(indole-3)-3-pentanol,1-(indole-3)-2-pentanone, 1-(indole-3)-3-pentanone,1-(indole-3)-2,3-pentanediol, 1-(indole-3)-2-hydroxy-3-pentanone,1-(indole-3)-3-hydroxy-2-pentanone, 1-(indole-3)-2,3-pentanedione,4-methyl-1-(indole-3-)pentane, 4-methyl-1-(indole-3)-2-pentene,4-methyl-1-(indole-3)-3-pentene, 4-methyl-1-(indole-3)-1-pentene,4-methyl-2-(indole-3)-3-pentanol, 4-methyl-1-(indole-3)-2-pentanol,4-methyl-1-(indole-3)-3-pentanone, 4-methyl-1-(indole-3)-2-pentanone,4-methyl-1-(indole-3)-2,3-pentanediol,4-methyl-1-(indole-3)-2,3-pentanedione,4-methyl-1-(indole-3)-3-hydroxy-2-pentanone,4-methyl-1-(indole-3)-2-hydroxy-3-pentanone, n-hexane, 1-hexene,1-hexanol, hexanal, hexanoate, 2-hexene, 3-hexene, 2-hexanol, 3-hexanol,2-hexanone, 3-hexanone, 2,3-hexanediol, 2,3-hexanedione, 3,4-hexanediol,3,4-hexanedione, 2-hydroxy-3-hexanone, 3-hydroxy-2-hexanone,3-hydroxy-4-hexanone, 4-hydroxy-3-hexanone, 2-methylhexane,3-methylhexane, 2-methyl-2-hexene, 2-methyl-3-hexene, 5-methyl-1-hexene,5-methyl-2-hexene, 4-methyl-1-hexene, 4-methyl-2-hexene,3-methyl-3-hexene, 3-methyl-2-hexene, 3-methyl-1-hexene,2-methyl-3-hexanol, 5-methyl-2-hexanol, 5-methyl-3-hexanol,2-methyl-3-hexanone, 5-methyl-2-hexanone, 5-methyl-3-hexanone,2-methyl-3,4-hexanediol, 2-methyl-3,4-hexanedione,5-methyl-2,3-hexanediol, 5-methyl-2,3-hexanedione,4-methyl-2,3-hexanediol, 4-methyl-2,3-hexanedione,2-methyl-3-hydroxy-4-hexanone, 2-methyl-4-hydroxy-3-hexanone,5-methyl-2-hydroxy-3-hexanone, 5-methyl-3-hydroxy-2-hexanone,4-methyl-2-hydroxy-3-hexanone, 4-methyl-3-hydroxy-2-hexanone,2,5-dimethylhexane, 2,5-dimethyl-2-hexene, 2,5-dimethyl-3-hexene,2,5-dimethyl-3-hexanol, 2,5-dimethyl-3-hexanone,2,5-dimethyl-3,4-hexanediol, 2,5-dimethyl-3,4-hexanedione,2,5-dimethyl-3-hydroxy-4-hexanone, 5-methyl-1-phenylhexane,4-methyl-1-phenylhexane, 5-methyl-1-phenyl-1-hexene,5-methyl-1-phenyl-2-hexene, 5-methyl-1-phenyl-3-hexene,4-methyl-1-phenyl-1-hexene, 4-methyl-1-phenyl-2-hexene,4-methyl-1-phenyl-3-hexene, 5-methyl-1-phenyl-2-hexanol,5-methyl-1-phenyl-3-hexanol, 4-methyl-1-phenyl-2-hexanol,4-methyl-1-phenyl-3-hexanol, 5-methyl-1-phenyl-2-hexanone,5-methyl-1-phenyl-3-hexanone, 4-methyl-1-phenyl-2-hexanone,4-methyl-1-phenyl-3-hexanone, 5-methyl-1-phenyl-2,3-hexanediol,4-methyl-1-phenyl-2,3-hexanediol,5-methyl-1-phenyl-3-hydroxy-2-hexanone,5-methyl-1-phenyl-2-hydroxy-3-hexanone,4-methyl-1-phenyl-3-hydroxy-2-hexanone,4-methyl-1-phenyl-2-hydroxy-3-hexanone,5-methyl-1-phenyl-2,3-hexanedione, 4-methyl-1-phenyl-2,3-hexanedione,4-methyl-1-(4-hydroxyphenyl)hexane,5-methyl-1-(4-hydroxyphenyl)-1-hexene,5-methyl-1-(4-hydroxyphenyl)-2-hexene,5-methyl-1-(4-hydroxyphenyl)-3-hexene,4-methyl-1-(4-hydroxyphenyl)-1-hexene,4-methyl-1-(4-hydroxyphenyl)-2-hexene,4-methyl-1-(4-hydroxyphenyl)-3-hexene,5-methyl-1-(4-hydroxyphenyl)-2-hexanol,5-methyl-1-(4-hydroxyphenyl)-3-hexanol,4-methyl-1-(4-hydroxyphenyl)-2-hexanol,4-methyl-1-(4-hydroxyphenyl)-3-hexanol,5-methyl-1-(4-hydroxyphenyl)-2-hexanone,5-methyl-1-(4-hydroxyphenyl)-3-hexanone,4-methyl-1-(4-hydroxyphenyl)-2-hexanone,4-methyl-1-(4-hydroxyphenyl)-3-hexanone,5-methyl-1-(4-hydroxyphenyl)-2,3-hexanediol,4-methyl-1-(4-hydroxyphenyl)-2,3-hexanediol,5-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-hexanone,5-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-hexanone,4-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-hexanone,4-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-hexanone,5-methyl-1-(4-hydroxyphenyl)-2,3-hexanedione,4-methyl-1-(4-hydroxyphenyl)-2,3-hexanedione,4-methyl-1-(indole-3-)hexane, 5-methyl-1-(indole-3)-1-hexene,5-methyl-1-(indole-3)-2-hexene, 5-methyl-1-(indole-3)-3-hexene,4-methyl-1-(indole-3)-1-hexene, 4-methyl-1-(indole-3)-2-hexene,4-methyl-1-(indole-3)-3-hexene, 5-methyl-1-(indole-3)-2-hexanol,5-methyl-1-(indole-3)-3-hexanol, 4-methyl-1-(indole-3)-2-hexanol,4-methyl-1-(indole-3)-3-hexanol, 5-methyl-1-(indole-3)-2-hexanone,5-methyl-1-(indole-3)-3-hexanone, 4-methyl-1-(indole-3)-2-hexanone,4-methyl-1-(indole-3)-3-hexanone, 5-methyl-1-(indole-3)-2,3-hexanediol,4-methyl-1-(indole-3)-2,3-hexanediol,5-methyl-1-(indole-3)-3-hydroxy-2-hexanone,5-methyl-1-(indole-3)-2-hydroxy-3-hexanone,4-methyl-1-(indole-3)-3-hydroxy-2-hexanone,4-methyl-1-(indole-3)-2-hydroxy-3-hexanone,5-methyl-1-(indole-3)-2,3-hexanedione,4-methyl-1-(indole-3)-2,3-hexanedione, n-heptane, 1-heptene, 1-heptanol,heptanal, heptanoate, 2-heptene, 3-heptene, 2-heptanol, 3-heptanol,4-heptanol, 2-heptanone, 3-heptanone, 4-heptanone, 2,3-heptanediol,2,3-heptanedione, 3,4-heptanediol, 3,4-heptanedione,2-hydroxy-3-heptanone, 3-hydroxy-2-heptanone, 3-hydroxy-4-heptanone,4-hydroxy-3-heptanone, 2-methylheptane, 3-methylheptane,6-methyl-2-heptene, 6-methyl-3-heptene, 2-methyl-3-heptene,2-methyl-2-heptene, 5-methyl-2-heptene, 5-methyl-3-heptene,3-methyl-3-heptene, 2-methyl-3-heptanol, 2-methyl-4-heptanol,6-methyl-3-heptanol, 5-methyl-3-heptanol, 3-methyl-4-heptanol,2-methyl-3-heptanone, 2-methyl-4-heptanone, 6-methyl-3-heptanone,5-methyl-3-heptanone, 3-methyl-4-heptanone, 2-methyl-3,4-heptanediol,2-methyl-3,4-heptanedione, 6-methyl-3,4-heptanediol,6-methyl-3,4-heptanedione, 5-methyl-3,4-heptanediol,5-methyl-3,4-heptanedione, 2-methyl-3-hydroxy-4-heptanone,2-methyl-4-hydroxy-3-heptanone, 6-methyl-3-hydroxy-4-heptanone,6-methyl-4-hydroxy-3-heptanone, 5-methyl-3-hydroxy-4-heptanone,5-methyl-4-hydroxy-3-heptanone, 2,6-dimethylheptane,2,5-dimethylheptane, 2,6-dimethyl-2-heptene, 2,6-dimethyl-3-heptene,2,5-dimethyl-2-heptene, 2,5-dimethyl-3-heptene, 3,6-dimethyl-3-heptene,2,6-dimethyl-3-heptanol, 2,6-dimethyl-4-heptanol,2,5-dimethyl-3-heptanol, 2,5-dimethyl-4-heptanol,2,6-dimethyl-3,4-heptanediol, 2,6-dimethyl-3,4-heptanedione,2,5-dimethyl-3,4-heptanediol, 2,5-dimethyl-3,4-heptanedione,2,6-dimethyl-3-hydroxy-4-heptanone, 2,6-dimethyl-4-hydroxy-3-heptanone,2,5-dimethyl-3-hydroxy-4-heptanone, 2,5-dimethyl-4-hydroxy-3-heptanone,n-octane, 1-octene, 2-octene, 1-octanol, octanal, octanoate, 3-octene,4-octene, 4-octanol, 4-octanone, 4,5-octanediol, 4,5-octanedione,4-hydroxy-5-octanone, 2-methyloctane, 2-methyl-3-octene,2-methyl-4-octene, 7-methyl-3-octene, 3-methyl-3-octene,3-methyl-4-octene, 6-methyl-3-octene, 2-methyl-4-octanol,7-methyl-4-octanol, 3-methyl-4-octanol, 6-methyl-4-octanol,2-methyl-4-octanone, 7-methyl-4-octanone, 3-methyl-4-octanone,6-methyl-4-octanone, 2-methyl-4,5-octanediol, 2-methyl-4,5-octanedione,3-methyl-4,5-octanediol, 3-methyl-4,5-octanedione,2-methyl-4-hydroxy-5-octanone, 2-methyl-5-hydroxy-4-octanone,3-methyl-4-hydroxy-5-octanone, 3-methyl-5-hydroxy-4-octanone,2,7-dimethyloctane, 2,7-dimethyl-3-octene, 2,7-dimethyl-4-octene,2,7-dimethyl-4-octanol, 2,7-dimethyl-4-octanone,2,7-dimethyl-4,5-octanediol, 2,7-dimethyl-4,5-octanedione,2,7-dimethyl-4-hydroxy-5-octanone, 2,6-dimethyloctane,2,6-dimethyl-3-octene, 2,6-dimethyl-4-octene, 3,7-dimethyl-3-octene,2,6-dimethyl-4-octanol, 3,7-dimethyl-4-octanol, 2,6-dimethyl-4-octanone,3,7-dimethyl-4-octanone, 2,6-dimethyl-4,5-octanediol,2,6-dimethyl-4,5-octanedione, 2,6-dimethyl-4-hydroxy-5-octanone,2,6-dimethyl-5-hydroxy-4-octanone, 3,6-dimethyloctane,3,6-dimethyl-3-octene, 3,6-dimethyl-4-octene, 3,6-dimethyl-4-octanol,3,6-dimethyl-4-octanone, 3,6-dimethyl-4,5-octanediol,3,6-dimethyl-4,5-octanedione, 3,6-dimethyl-4-hydroxy-5-octanone,n-nonane, 1-nonene, 1-nonanol, nonanal, nonanoate, 2-methylnonane,2-methyl-4-nonene, 2-methyl-5-nonene, 8-methyl-4-nonene,2-methyl-5-nonanol, 8-methyl-4-nonanol, 2-methyl-5-nonanone,8-methyl-4-nonanone, 8-methyl-4,5-nonanediol, 8-methyl-4,5-nonanedione,8-methyl-4-hydroxy-5-nonanone, 8-methyl-5-hydroxy-4-nonanone,2,8-dimethylnonane, 2,8-dimethyl-3-nonene, 2,8-dimethyl-4-nonene,2,8-dimethyl-5-nonene, 2,8-dimethyl-4-nonanol, 2,8-dimethyl-5-nonanol,2,8-dimethyl-4-nonanone, 2,8-dimethyl-5-nonanone,2,8-dimethyl-4,5-nonanediol, 2,8-dimethyl-4,5-nonanedione,2,8-dimethyl-4-hydroxy-5-nonanone, 2,8-dimethyl-5-hydroxy-4-nonanone,2,7-dimethylnonane, 3,8-dimethyl-3-nonene, 3,8-dimethyl-4-nonene,3,8-dimethyl-5-nonene, 3,8-dimethyl-4-nonanol, 3,8-dimethyl-5-nonanol,3,8-dimethyl-4-nonanone, 3,8-dimethyl-5-nonanone,3,8-dimethyl-4,5-nonanediol, 3,8-dimethyl-4,5-nonanedione,3,8-dimethyl-4-hydroxy-5-nonanone, 3,8-dimethyl-5-hydroxy-4-nonanone,n-decane, 1-decene, 1-decanol, decanoate, 2,9-dimethyldecane,2,9-dimethyl-3-decene, 2,9-dimethyl-4-decene, 2,9-dimethyl-5-decanol,2,9-dimethyl-5-decanone, 2,9-dimethyl-5,6-decanediol,2,9-dimethyl-6-hydroxy-5-decanone,2,9-dimethyl-5,6-decanedionen-undecane, 1-undecene, 1-undecanol,undecanal. undecanoate, n-dodecane, 1-dodecene, 1-dodecanol, dodecanal,dodecanoate, n-dodecane, 1-decadecene, 1-dodecanol, ddodecanal,dodecanoate, n-tridecane, 1-tridecene, 1-tridecanol, tridecanal,tridecanoate, n-tetradecane, 1-tetradecene, 1-tetradecanol,tetradecanal, tetradecanoate, n-pentadecane, 1-pentadecene,1-pentadecanol, pentadecanal, pentadecanoate, n-hexadecane,1-hexadecene, 1-hexadecanol, hexadecanal, hexadecanoate, n-heptadecane,1-heptadecene, 1-heptadecanol, heptadecanal, heptadecanoate,n-octadecane, 1-octadecene, 1-octadecanol, octadecanal, octadecanoate,n-nonadecane, 1-nonadecene, 1-nonadecanol, nonadecanal, nonadecanoate,eicosane, 1-eicosene, 1-eicosanol, eicosanal, eicosanoate, 3-hydroxypropanal, 1,3-propanediol, 4-hydroxybutanal, 1,4-butanediol,3-hydrxy-2-butanone, 2,3-butandiol, 1,5-pentane diol, homocitrate,homoisocitorate, b-hydroxy adipate, glutarate, glutarsemialdehyde,glutaraldehyde, 2-hydroxy-1-cyclopentanone, 1,2-cyclopentanediol,cyclopentanone, cyclopentanol, (S)-2-acetolactate,(R)-2,3-Dihydroxy-isovalerate, 2-oxoisovalerate, isobutyryl-CoA,isobutyrate, isobutyraldehyde, 5-amino pentaldehyde, 1,10-diaminodecane,1,10-diamino-5-decene, 1,10-diamino-5-hydroxydecane,1,10-diamino-5-decanone, 1,10-diamino-5,6-decanediol,1,10-diamino-6-hydroxy-5-decanone, phenylacetoaldehyde,1,4-diphenylbutane, 1,4-diphenyl-1-butene, 1,4-diphenyl-2-butene,1,4-diphenyl-2-butanol, 1,4-diphenyl-2-butanone,1,4-diphenyl-2,3-butanediol, 1,4-diphenyl-3-hydroxy-2-butanone,1-(4-hydeoxyphenyl)-4-phenylbutane,1-(4-hydeoxyphenyl)-4-phenyl-1-butene,1-(4-hydeoxyphenyl)-4-phenyl-2-butene,1-(4-hydeoxyphenyl)-4-phenyl-2-butanol,1-(4-hydeoxyphenyl)-4-phenyl-2-butanone,1-(4-hydeoxyphenyl)-4-phenyl-2,3-butanediol,1-(4-hydeoxyphenyl)-4-phenyl-3-hydroxy-2-butanone,1-(indole-3)-4-phenylbutane, 1-(indole-3)-4-phenyl-1-butene,1-(indole-3)-4-phenyl-2-butene, 1-(indole-3)-4-phenyl-2-butanol,1-(indole-3)-4-phenyl-2-butanone, 1-(indole-3)-4-phenyl-2,3-butanediol,1-(indole-3)-4-phenyl-3-hydroxy-2-butanone,4-hydroxyphenylacetoaldehyde, 1,4-di(4-hydroxyphenyl)butane,1,4-di(4-hydroxyphenyl)-1-butene, 1,4-di(4-hydroxyphenyl)-2-butene,1,4-di(4-hydroxyphenyl)-2-butanol, 1,4-di(4-hydroxyphenyl)-2-butanone,1,4-di(4-hydroxyphenyl)-2,3-butanediol,1,4-di(4-hydroxyphenyl)-3-hydroxy-2-butanone,1-(4-hydroxyphenyl)-4-(indole-3-)butane,1-(4-hydroxyphenyl)-4-(indole-3)-1-butene,1-di(4-hydroxyphenyl)-4-(indole-3)-2-butene,1-(4-hydroxyphenyl)-4-(indole-3)-2-butanol,1-(4-hydroxyphenyl)-4-(indole-3)-2-butanone,1-(4-hydroxyphenyl)-4-(indole-3)-2,3-butanediol,1-(4-hydroxyphenyl-4-(indole-3)-3-hydroxy-2-butanone,indole-3-acetoaldehyde, 1,4-di(indole-3-)butane,1,4-di(indole-3)-1-butene, 1,4-di(indole-3)-2-butene,1,4-di(indole-3)-2-butanol, 1,4-di(indole-3)-2-butanone,1,4-di(indole-3)-2,3-butanediol, 1,4-di(indole-3)-3-hydroxy-2-butanone,succinate semialdehyde, hexane-1,8-dicarboxylic acid,3-hexene-1,8-dicarboxylic acid, 3-hydroxy-hexane-1,8-dicarboxylic acid,3-hexanone-1,8-dicarboxylic acid, 3,4-hexanediol-1,8-dicarboxylic acid,4-hydroxy-3-hexanone-1,8-dicarboxylic acid, fucoidan, iodine,chlorophyll, carotenoid, calcium, magnesium, iron, sodium, potassium,and phosphate.

Certain embodiments of the present invention include methods forconverting a polysaccharide to a suitable monosaccharide oroligosaccharide, comprising: (a) contacting the polysaccharide, whereinthe polysaccharide is optionally obtained from biomass, with a microbialsystem for a time sufficient to convert the polysaccharide to a suitablemonosaccharide or oligosaccharide, wherein the microbial systemcomprises, (i) at least one gene encoding and expressing an enzymeselected from a lyase and a hydrolase, wherein the lyase and/orhydrolase optionally comprises at least one signal peptide or at leastone autotransporter domain; (ii) at least one gene encoding andexpressing an enzyme selected from a monosaccharide transporter, adisaccharide transporter, a trisaccharide transporter, anoligosaccharide transporter, a polysaccharide transporter, and asuperchannel; and (iii) at least one gene encoding and expressing anenzyme selected from a monosaccharide dehydrogenase, an isomerase, adehydratase, a kinase, and an aldolase, thereby converting thepolysaccharide to a suitable monosaccharide or oligosaccharide.

Certain embodiments of the present invention include methods forconverting a polysaccharide to a suitable monosaccharide oroligosaccharide, comprising: (a) contacting the polysaccharide, whereinthe polysaccharide is optionally obtained from biomass, with a chemicalor enzymatic catalysis pathway for a time sufficient to convert thepolysaccharide to a first monosaccharide or oligosaccharide; and (b)contacting the first monosaccharide or oligosaccharide with a microbialsystem for a time sufficient to convert the first monosaccharide oroligosaccharide to the suitable monosaccharide or oligosaccharide,wherein the microbial system comprises, (i) at least one gene encodingand expressing an enzyme selected from a lyase and a hydrolase, (ii) atleast one gene encoding and expressing an enzyme selected from amonosaccharide transporter, a disaccharide transporter, a trisaccharidetransporter, an oligosaccharide transporter, a polysaccharidetransporter, and a superchannel; and (ii) at least one gene encoding andexpressing an enzyme selected from a monosaccharide dehydrogenase, anisomerase, a dehydratase, a kinase, and an aldolase, thereby convertingthe polysaccharide to the suitable monosaccharide or oligosaccharide.

In certain aspects, the lyase is selected from an alginate lyase, apectate lyase, a polymannuronate lyase, a polygluronate lyase, apolygalacturonate lyase and a rhamnogalacturonate lyase. In certainaspects, the hydrolase is selected from an alginate hydrolase, arhamnogalacturonate hydrolase, a polymannuronate hydrolase, a pectinhydrolase, and a polygalacturonate hydrolase. In certain aspects, thetransporter is selected from an ABC transporter, a symporter, and anouter membrane porin. In certain aspects, the ABC transporter isselected from Atu3021, Atu3022, Atu3023, Atu3024, algM1, algM2, AlgQ1,AlgQ2, AlgS, OG2516_(—)05558, OG2516_(—)05563, OG2516_(—)05568,OG2516_(—)05573, TogM, TogN, TogA, TogB, and functional variantsthereof. In certain aspects, the symporter is selected fromV12B01_(—)24239 (SEQ ID NO:26), V12B01_(—)24194 (SEQ ID NO:8), and TogT,and functional variants thereof. In certain aspects, the outermembraneporin comprises a porin selected from V12B01_(—)24269, KdgM, and KdgN,and functional variants thereof.

Certain embodiments include a recombinant microorganism that is capableof growing on a polysaccharide as a sole source of carbon, wherein thepolysaccharide is selected from alginate, pectin, tri-galacturonate,di-galacturonate, cellulose, and hemi-cellulose. In certain aspects, thepolysaccharide is alginate. In certain aspects, the polysaccharide ispectin. In certain aspects, the polysaccharide is tri-galacturonate.

Certain embodiments include a recombinant microrganism, comprising (i)at least one gene encoding and expressing an enzyme selected from alyase and a hydrolase, wherein the lyase or hydrolase optionallycomprises at least one signal peptide or at least one autotransporterdomain; (ii) at least one gene encoding and expressing an enzymeselected from a monosaccharide transporter, a disaccharide transporter,a trisaccharide transporter, an oligosaccharide transporter, apolysaccharide transporter, and a superchannel; and (iii) at least onegene encoding and expressing an enzyme selected from a monosaccharidedehydrogenase, an isomerase, a dehydratase, a kinase, and an aldolase.In certain aspects, the microorganism is capable of growing on apolysaccharide as a sole source of carbon. In certain aspects, thepolysaccharide is selected from alginate, pectin, and tri-galacturonate.

Certain embodiments include methods for converting a suitablemonosaccharide or oligosaccharide to a first commodity chemicalcomprising, (a) contacting the suitable monosaccharide oroligosaccharide with a microbial system for a time sufficient to convertto the suitable monosaccharide or oligosaccharide to the commoditychemical, wherein the microbial system comprises a recombinantmicroorganism, wherein the microorganism comprises a commodity chemicalbiosynthesis pathway, thereby converting the suitable monosaccharide oroligosaccharide to the first commodity chemical. In certain aspects, thecommodity chemical pathway comprises one or more genes encoding analdehyde or ketone biosynthesis pathway.

In certain aspects, the aldehyde or ketone biosynthesis pathway isselected from one or more of an acetoaldehyde, a propionaldehyde, abutyraldehyde, an isobutyraldehyde, a 2-methyl-butyraldehyde, a3-methyl-butyraldehyde, a 2-phenyl acetaldehyde, a2-(4-hydroxyphenyl)acetaldehyde, a 2-Indole-3-acetoaldehyde, aglutaraldehyde, a 5-amino-pentaldehyde, a succinate semialdehyde, and asuccinate 4-hydroxyphenyl acetaldehyde biosynthesis pathway. In certainaspects, the aldehyde or ketone biosynthesis pathway comprises anacetoaldehyde biosynthesis pathway and a biosynthesis pathway selectedfrom a propionaldehyde, butyraldehyde, isobutyraldehyde,2-methyl-butyraldehyde, 3-methyl-butyraldehyde, a 2-phenylacetoaldehyde, a 2-(4-hydroxyphenyl)acetaldehyde, and a2-Indole-3-acetoaldehyde biosynthesis pathway.

In certain aspects, the aldehyde or ketone biosynthesis pathwaycomprises a propionaldehyde biosynthesis pathway and a biosynthesispathway selected from a butyraldehyde, isobutyraldehyde,2-methyl-butyraldehyde, 3-methyl-butyraldehyde, and phenylacetoaldehydebiosynthesis pathway. In certain aspects, the aldehyde or ketonebiosynthesis pathway comprises a butyraldehyde biosynthesis pathway anda biosynthesis pathway selected from an isobutyraldehyde,2-methyl-butyraldehyde, 3-methyl-butyraldehyde, a 2-phenylacetoaldehyde, a 2-(4-hydroxyphenyl)acetaldehyde, and a2-Indole-3-acetoaldehyde biosynthesis pathway. In certain aspects, thealdehyde or ketone biosynthesis pathway comprises an isobutyraldehydebiosynthesis pathway and a biosynthesis pathway selected from a2-methyl-butyraldehyde, 3-methyl-butyraldehyde, a 2-phenylacetoaldehyde, a 2-(4-hydroxyphenyl)acetaldehyde, and a2-Indole-3-acetoaldehyde biosynthesis pathway.

In certain aspects, the aldehyde or ketone biosynthesis pathwaycomprises a 2-methyl-butyraldehyde biosynthesis pathway and abiosynthesis pathway selected from a 3-methyl-butyraldehyde, a 2-phenylacetoaldehyde, a 2-(4-hydroxyphenyl)acetaldehyde, and a2-Indole-3-acetoaldehyde biosynthesis pathway. In certain aspects, thealdehyde or ketone biosynthesis pathway comprises a3-methyl-butyraldehyde biosynthesis pathway and a biosynthesis pathwayselected from a 2-phenyl acetoaldehyde, a2-(4-hydroxyphenyl)acetaldehyde, and a 2-Indole-3-acetoaldehydebiosynthesis pathway. In certain aspects, the aldehyde or ketonebiosynthesis pathway comprises a 2-phenyl acetoaldehyde biosynthesispathway and a biosynthesis pathway selected from a2-(4-hydroxyphenyl)acetaldehyde and a 2-Indole-3-acetoaldehydebiosynthesis pathway.

In certain aspects, the aldehyde or ketone biosynthesis pathwaycomprises a 2-(4-hydroxyphenyl)acetaldehyde biosynthesis pathway and a2-Indole-3-acetoaldehyde biosynthesis pathway. In certain aspects, thefirst commodity chemical is further enzymatically and/or chemicallyreduced and dehydrated to a second commodity chemical.

Certain embodiments include methods for converting a suitablemonosaccharide or oligosaccharide to a commodity chemical comprising,(a) contacting the suitable monosaccharide or oligosaccharide with amicrobial system for a time sufficient to convert to the suitablemonosaccharide or oligosaccharide to the commodity chemical, wherein themicrobial system comprises; (i) one or more genes encoding andexpressing an aldehyde biosynthesis pathway, wherein the aldehydebiosynthesis pathway comprises one or more genes encoding and expressinga decarboxylase enzyme; and (ii)

one or more genes encoding and expressing an aldehyde reductase, therebyconverting the suitable monosaccharide or oligosaccharide to thecommodity chemical. In certain aspects, the decarboxylase enzyme is anindole-3-pyruvate decarboxylase (IPDC). In certain aspects, the IPDCcomprises an amino acid sequence that is at least 80%, 90%, 95%, 98%, or99% identical to the amino acid sequence set forth in SEQ ID NO: 312. Incertain aspects, the aldehyde reductase enzyme is a phenylacetaldehydereductase (PAR). In certain aspects, the PAR comprises an amino acidsequence that is at least 80%, 90%, 95%, 98%, or 99% identical to theamino acid sequence set forth in SEQ ID NO: 313. In certain aspects, thecommodity chemical is selected from 2-phenylethanol,2-(4-hydroxyphenyl)ethanol, and indole-3-ethanol.

Certain embodiments include a recombinant microorganism, comprising (i)one or more genes encoding and expressing an aldehyde biosynthesispathway, wherein the aldehyde biosynthesis pathway comprises one or moregenes encoding and expressing a decarboxylase enzyme; and (ii) one ormore genes encoding and expressing an aldehyde reductase. In certainaspects, the aldehyde biosynthesis pathway further comprises one or moregenes encoding and expressing an enzyme selected from a CoA-linkedaldehyde dehydrogenase, an aldehyde dehydrogenase, and an alcoholdehydrogenase. In certain aspects, the decarboxylase enzyme is anindole-3-pyruvate decarboxylase (IPDC). In certain aspects, the aldehydereductase enzyme is a phenylacetoaldehyde reductase (PAR). In certainaspects, the microorganism is capable of converting a suitablemonosaccharide or oligosaccharide to a commodity chemical. In certainaspects, the commodity chemical is selected from 2-phenylethanol,2-(4-hydroxyphenyl)ethanol, and indole-3-ethanol.

Certain embodiments include a recombinant microorganism, wherein themicroorganism comprises reduced ethanol production capability comparedto a wild-type microorganism. In certain aspects, the microorganismcomprises a reduction or inhibition in the conversion of acetyl-coA toethanol. In certain aspects, the recombinant microorganism comprises areduction of an ethanol dehydrogenase, thereby providing a reducedethanol production capability. In certain aspects, the ethanoldehydrogenase is an adhE, homolog or variant thereof. In certainaspects, the microorganism comprises a deletion or knockout of an adhE,homolog or variant thereof. In certain aspects, the recombinantmicroorganism comprises one or more deletions or knockouts in a geneencoding an enzyme selected from an enzyme that catalyzes the conversionof acetyl-coA to ethanol, an enzyme that catalyzes the conversion ofpyruvate to lactate, an enzyme that catalyzes the conversion of fumarateto succinate, an enzyme that catalyzes the conversion of acetyl-coA andphosphate to coA and acetyl phosphate, an enzyme that catalyzes theconversion of acetyl-coA and formate to coA and pyruvate, and an enzymethat catalyzes the conversion of alpha-keto acid to branched chain aminoacids.

Certain embodiments include wherein the microbial systems or recombinantmicroorganisms described herein comprise a microorganism selected fromAcetobacter aceti, Achromobacter, Acidiphilium, Acinetobacter,Actinomadura, Actinoplanes, Aeropyrum pernix, Agrobacterium,Alcaligenes, Ananas comosus (M), Arthrobacter, Aspargillus niger,Aspargillus oryze, Aspergillus melleus, Aspergillus pulverulentus,Aspergillus saitoi, Aspergillus sojea, Aspergillus usamii, Bacillusalcalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacilluscirculans, Bacillus clausii, Bacillus lentus, Bacillus licheniformis,Bacillus macerans, Bacillus stearothermophilus, Bacillus subtilis,Bifidobacterium, Brevibacillus brevis, Burkholderia cepacia, Candidacylindracea, Candida rugosa, Carica papaya (L), Cellulosimicrobium,Cephalosporium, Chaetomium erraticum, Chaetomium gracile, Clostridium,Clostridium butyricum, Clostridium acetobutylicum, Clostridiumthermocellum, Corynebacterium (glutamicum), Corynebacterium efficiens,Escherichia coli, Enterococcus, Erwina chrysanthemi, Gliconobacter,Gluconacetobacter, Haloarcula, Humicola insolens, Humicola nsolens,Kitasatospora setae, Klebsiella, Klebsiella oxytoca, Kluyveromyces,Kluyveromyces fragilis, Kluyveromyces lactis, Kocuria, Lactlactis,Lactobacillus, Lactobacillus fermentum, Lactobacillus sake, Lactococcus,Lactococcus lactis, Leuconostoc, Methylocystis, Methanolobus siciliae,Methanogenium organophilum, Methanobacterium bryantii, Microbacteriumimperiale, Micrococcus lysodeikticus, Microlunatus, Mucor javanicus,Mycobacterium, Myrothecium, Nitrobacter, Nitrosomonas, Nocardia, Papayacarica, Pediococcus, Pediococcus halophilus, Penicillium, Penicilliumcamemberti, Penicillium citrinum, Penicillium emersonii, Penicilliumroqueforti, Penicillum lilactinum, Penicillum multicolor, Paracoccuspantotrophus, Propionibacterium, Pseudomonas, Pseudomonas fluorescens,Pseudomonas denitrificans, Pyrococcus, Pyrococcus furiosus, Pyrococcushorikoshii, Rhizobium, Rhizomucor miehei, Rhizomucor pusillus Lindt,Rhizopus, Rhizopus delemar, Rhizopus japonicus, Rhizopus niveus,Rhizopus oryzae, Rhizopus oligosporus, Rhodococcus, Sccharomycescerevisiae, Sclerotina libertina, Sphingobacterium multivorum,Sphingobium, Sphingomonas, Streptococcus, Streptococcus thermophilusY-1, Streptomyces, Streptomyces griseus, Streptomyces lividans,Streptomyces murinus, Streptomyces rubiginosus, Streptomycesviolaceoruber, Streptoverticillium mobaraense, Tetragenococcus, Thermus,Thiosphaera pantotropha, Trametes, Trichoderma, Trichodermalongibrachiatum, Trichoderma reesei, Trichoderma viride, Trichosporonpenicillatum, Vibrio alginolyticus, Xanthomonas, yeast,Zygosaccharomyces rouxii, Zymomonas, and Zymomonus mobilis.

Certain embodiments include a commodity chemical produced by the methodsdescribed herein. Certain aspects include a blended commodity chemicalcomprising a commodity chemical produced by the methods provided hereinand a refinery-produced petroleum product. In certain aspects, thecommodity chemical is selected from a C10-C12 hydrocarbon,2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and indole-3-ethanol. Incertain aspects, the C10-C12 hydrocarbon is selected from2,7-dimethyloctane and 2,9-dimethyldecane. In certain aspects, therefinery-produced petroleum product is selected from jet fuel and dieselfuel.

Certain embodiments include methods of producing a commodity chemicalenriched refinery-produced petroleum product, comprising (a) blendingthe refinery-produced petroleum product with the commodity chemicalproduced by the methods described herein, thereby producing thecommodity chemical enriched refinery-produced petroleum product.

DETAILED DESCRIPTION

Embodiments of the present invention relate to the unexpected discoverythat microorganisms which are otherwise incapable of growing on certainpolysaccharides derived from biomass as a sole source of carbon, can beengineered to grow on these polysaccharides as a sole source of carbon.Such microorganisms can include both prokaryotic and eukaryoticmicroorganisms, such as bacteria and yeast. In some aspects, certainlaboratory and/or wild-type strains of E. coli can be engineered to growon biomass derived from either alginate or pectin as a sole source ofcarbon to produce suitable monosaccharides or other molecules. Amongother uses apparent to a person skilled in the art, the monosaccharidesand other molecules produced by the growth of these engineered orrecombinant microorganisms on alginate or pectin may be utilized asfeedstock in the production of various commodity chemicals, such asbiofuels.

Alginate and pectin provide advantages over other biomass sources in theproduction of biofuel feedstocks. For example, large-scaleaquatic-farming can generate a significant amount of biomass withoutreplacing food crop production with energy crop production,deforestation, and recultivating currently uncultivated land, as most ofhydrosphere including oceans, rivers, and lakes remains untapped. As oneparticular example, the Pacific coast of North America is abundant inminerals necessary for large-scale aqua-farming. Giant kelp, which livesin the area, grows as fast as 1 m/day, the fastest among plants onearth, and grows up to 50 m. Additionally, aqua-farming has otherbenefits including the prevention of a red tide outbreak and thecreation of a fish-friendly environment.

As an additional advantage, and in contrast to lignocellulolic biomass,biomass derived from aquatic, fruit, plant and/or vegetable sources iseasy to degrade. Such biomass typically lacks lignin and issignificantly more fragile than lignocellulolic biomass and can thus beeasily degraded using either enzymes or chemical catalysts (e.g.,formate). As one example, aquatic biomass such as seaweed may be easilyconverted to monosaccharides using either enzymes or chemical catalysis,as seaweed has significantly simpler major sugar components (Alginate:30%, Mannitol: 15%) as compared to lignocellulose (Glucose: 24.1-39%,Mannose: 0.2-4.6%, Galactose: 0.5-2.4%, Xylose: 0.4-22.1%, Arabinose1.5-2.8%, and Uronic acids: 1.2-20.7%, and total sugar contents arecorresponding to 36.5-70% of dried weight).

As an additional example, biomass from plants such as fruit and/orvegetable contains pectin, a heteropolysaccharide derived from the plantcell wall. The characteristic structure of pectin is a linear chain ofα-(1-4)-linked D-galacturonic acid that forms the pectin-backbone, ahomogalacturonan. Pectin can be easily converted to oligosaccharides orsuitable monosaccharides using either enzymes, chemical catalysis,and/or microbial systems designed to utilize pectin as a source ofcarbon, as described herein. Saccharification and fermentation usingaquatic, fruit, and/or vegetable biomass is much easier than usinglignocellulose.

In this regard, embodiments of the present invention also relate to thesurprising discovery that certain microorganisms can be engineered toproduce various commodity chemicals, such as biofuels. In certainaspects, these biofuels may include alkanes, such as medium to longchain alkanes, which provide advantages over ethanol based biofuels. Incertain aspects, the monosaccharides (e.g., 2-keto-3-deoxy D-gluconate;KDG) and other molecules produced by the growth of various engineered orrecombinant microorganisms (e.g., recombinant microorganisms growing onpectin or alginate as a source of carbon) may be useful in theproduction of commodity chemicals, such as biofuels. As one example,suitable monosaccharides such as KDG may be utilized by recombinantmicroorganisms to produce alkanes, such as medium to long chain alkanes,among other chemicals. In certain aspects, such recombinantmicroorganisms may be utilized to produce such commodity chemical as 2,7dimethyl octane and 2,9 dimethyl decane, among others provided hereinand known in the art.

Such processes produce biofuels with significant advantages over otherbiofuels. In particular, medium to long chain alkanes provide a numberof important advantages over the existing common biofuels such asethanol and butanol, and are attractive long-term replacements ofpetroleum-based fuels such as gasoline, diesels, kerosene, and heavyoils in the future. As one example, medium to long chain alkanes andalcohols are major components in all petroleum products and jet fuel inparticular, and hence alkanes we produce can be utilized directly byexisting engines. By way of further example, medium to long chainalcohols are far better fuels than ethanol, and have a nearly comparableenergy density to gasoline.

As another example, n-alkanes are major components of all oil productsincluding gasoline, diesels, kerosene, and heavy oils. Microbial systemsor recombinant microorganisms may be used to produce n-alkanes withdifferent carbon lengths ranging, for example, from C7 to over C20: C7for gasoline (e.g., motor vehicles), C10-C15 for diesels (e.g., motorvehicles, trains, and ships), and C8-C16 for kerosene (e.g., aviationsand ships), and for all heavy oils.

As one aspect of the invention, the commodity chemicals produced by themethods and recombinant microorganisms described herein may be utilizedby existing petroleum refineries for the purposes of blending withpetroleum products produced by traditional refinery methods. To thisend, as noted above, fuel producers are seeking substantially similar,low carbon fuels that can be blended and distributed through existinginfrastructure (refineries, pipelines, tankers). As hydrocarbons, thecommodity chemicals produced according to the methods herein aresubstantially similar to petroleum derived fuels, reduce green house gasemissions by more than 80% from petroleum derived fuels, and arecompatible with existing infrastructure in the oil and gas industry. Forinstance, certain of the commodity chemicals produced herein, including,for example, various C10-C12 hydrocarbons such as 2,7 dimethyloctane,2,7 dimethyldecanone, among others, are blendable directly intorefinery-produced petroleum products, such as jet and diesel fuels. Byusing such biologically produced commodity chemicals as a blendstock forjet and diesel fuels, refineries may reduce Green House Gas emissions bymore than 80%.

Accordingly, certain embodiments of the present invention relategenerally to methods for converting biomass to a commodity chemical,comprising obtaining a polysaccharide from biomass; contacting thepolysaccharide with a polysaccharide degrading or depolymerizingpathway, thereby converting the polysaccharide to a suitablemonosaccharide. The suitable monosaccharide obtained from such asprocess may be used for any desired purpose. For instance, in certainaspects, the suitable monosaccharide may then be converted to acommodity chemical (e.g., biofuel) by contacting the suitablemonosaccharide with a biofuel biosynthesis pathway, whether as part of arecombinant microorganism, an in vitro enzymatic or chemical pathway, ora combination thereof, thereby converting the monosaccharide to acommodity chemical.

In other aspects, in producing a commodity chemical such as a biofuel, asuitable monosaccharide may be obtained directly from any availablesource and converted to a commodity chemical by contacting the suitablemonosaccharide with a biofuel biosynthesis pathway, as described herein.Among other uses apparent to a person skilled in the art, such biofuelsmay then be blended directly with refinery produced petroleum products,such as jet and diesel fuels, to produce commodity chemical enriched,refinery-produced petroleum products.

DEFINITIONS

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by those of ordinary skillin the art to which the invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, preferred methods andmaterials are described. For the purposes of the present invention, thefollowing terms are defined below. All references referred to herein areincorporated by reference in their entirety.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e. to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element.

By “about” is meant a quantity, level, value, number, frequency,percentage, dimension, size, amount, weight or length that varies by asmuch as 30, 25, 20, 25, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1% to a referencequantity, level, value, number, frequency, percentage, dimension, size,amount, weight or length.

The term “biologically active fragment”, as applied to fragments of areference polynucleotide or polypeptide sequence, refers to a fragmentthat has at least about 0.1, 0.5, 1, 2, 5, 10, 12, 14, 16, 18, 20, 22,24, 26, 28, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96,97, 98, 99, 100, 110, 120, 150, 200, 300, 400, 500, 600, 700, 800, 900,1000% or more of the activity of a reference sequence.

The term “reference sequence” refers generally to a nucleic acid codingsequence, or amino acid sequence, of any enzyme having a biologicalactivity described herein (e.g., saccharide dehydrogenase, alcoholdehydrogenase, dehydratase, lyase, transporter, decarboxylase,hydrolase, etc.), such as a “wild-type” sequence, including thosereference sequences exemplified by SEQ ID NOS:1-144, and 308-313. Areference sequence may also include naturally-occurring, functionalvariants (i.e., orthologs or homologs) of the sequences describedherein.

Included within the scope of the present invention are biologicallyactive fragments of at least about 18, 19, 20, 21, 22, 23, 24, 25, 26,27, 28, 29, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200,220, 240, 260, 280, 300, 320, 340, 360, 380, 400, 500, 600 or morecontiguous nucleotides or amino acid residues in length, including allintegers in between, which comprise or encode a polypeptide having anenzymatic activity of a reference polynucleotide or polypeptide.Representative biologically active fragments generally participate in aninteraction, e.g., an intra-molecular or an inter-molecular interaction.An inter-molecular interaction can be a specific binding interaction oran enzymatic interaction. Examples of enzymatic interactions oractivities include saccharide dehydrogenase activities, alcoholdehydrogenase activities, dehydratases activities, lyase activities,transporter activities, isomerase activities, kinase activities, amongothers described herein. Biologically active fragments typicallycomprise one or more active sites or enzymatic/binding motifs, asdescribed herein and known in the art.

By “coding sequence” is meant any nucleic acid sequence that contributesto the code for the polypeptide product of a gene. By contrast, the term“non-coding sequence” refers to any nucleic acid sequence that does notcontribute to the code for the polypeptide product of a gene.

Throughout this specification, unless the context requires otherwise,the words “comprise”, “comprises” and “comprising” will be understood toimply the inclusion of a stated step or element or group of steps orelements but not the exclusion of any other step or element or group ofsteps or elements.

By “consisting of,” is meant including, and limited to, whatever followsthe phrase “consisting of” Thus, the phrase “consisting of” indicatesthat the listed elements are required or mandatory, and that no otherelements may be present.

By “consisting essentially of” is meant including any elements listedafter the phrase, and limited to other elements that do not interferewith or contribute to the activity or action specified in the disclosurefor the listed elements. Thus, the phrase “consisting essentially of”indicates that the listed elements are required or mandatory, but thatother elements are optional and may or may not be present depending uponwhether or not they affect the activity or action of the listedelements.

The terms “complementary” and “complementarity” refer to polynucleotides(i.e., a sequence of nucleotides) related by the base-pairing rules. Forexample, the sequence “A-G-T,” is complementary to the sequence “T-C-A.”Complementarity may be “partial,” in which only some of the nucleicacids' bases are matched according to the base pairing rules. Or, theremay be “complete” or “total” complementarity between the nucleic acids.The degree of complementarity between nucleic acid strands hassignificant effects on the efficiency and strength of hybridizationbetween nucleic acid strands.

By “corresponds to” or “corresponding to” is meant (a) a polynucleotidehaving a nucleotide sequence that is substantially identical orcomplementary to all or a portion of a reference polynucleotide sequenceor encoding an amino acid sequence identical to an amino acid sequencein a peptide or protein; or (b) a peptide or polypeptide having an aminoacid sequence that is substantially identical to a sequence of aminoacids in a reference peptide or protein.

By “derivative” is meant a polypeptide that has been derived from thebasic sequence by modification, for example by conjugation or complexingwith other chemical moieties (e.g., pegylation) or by post-translationalmodification techniques as would be understood in the art. The term“derivative” also includes within its scope alterations that have beenmade to a parent sequence including additions or deletions that providefor functionally equivalent molecules.

By “enzyme reactive conditions” it is meant that any necessaryconditions are available in an environment (i.e., such factors astemperature, pH, lack of inhibiting substances) which will permit theenzyme to function. Enzyme reactive conditions can be either in vitro,such as in a test tube, or in vivo, such as within a cell.

As used herein, the terms “function” and “functional” and the like referto a biological or enzymatic function.

By “gene” is meant a unit of inheritance that occupies a specific locuson a chromosome and consists of transcriptional and/or translationalregulatory sequences and/or a coding region and/or non-translatedsequences (i.e., introns, 5′ and 3′ untranslated sequences).

“Homology” refers to the percentage number of amino acids that areidentical or constitute conservative substitutions. Homology may bedetermined using sequence comparison programs such as GAP (Deveraux etal., 1984, Nucleic Acids Research 12, 387-395) which is incorporatedherein by reference. In this way sequences of a similar or substantiallydifferent length to those cited herein could be compared by insertion ofgaps into the alignment, such gaps being determined, for example, by thecomparison algorithm used by GAP.

The term “host cell” includes an individual cell or cell culture whichcan be or has been a recipient of any recombinant vector(s) or isolatedpolynucleotide of the invention. Host cells include progeny of a singlehost cell, and the progeny may not necessarily be completely identical(in morphology or in total DNA complement) to the original parent celldue to natural, accidental, or deliberate mutation and/or change. A hostcell includes cells transfected, transformed, or infected in vivo or invitro with a recombinant vector or a polynucleotide of the invention. Ahost cell which comprises a recombinant vector of the invention is arecombinant host cell, recombinant cell, or recombinant microrganism.

By “isolated” is meant material that is substantially or essentiallyfree from components that normally accompany it in its native state. Forexample, an “isolated polynucleotide”, as used herein, refers to apolynucleotide, which has been purified from the sequences which flankit in a naturally-occurring state, e.g., a DNA fragment which has beenremoved from the sequences that are normally adjacent to the fragment.Alternatively, an “isolated peptide” or an “isolated polypeptide” andthe like, as used herein, refer to in vitro isolation and/orpurification of a peptide or polypeptide molecule from its naturalcellular environment, and from association with other components of thecell, i.e., it is not associated with in vivo substances.

By “increased” or “increasing” is meant the ability of one or morerecombinant microorganisms to produce a greater amount of a givenproduct or molecule (e.g., commodity chemical, biofuel, or intermediateproduct thereof) as compared to a control microorganism, such as anunmodified microorganism or a differently modified microorganism. An“increased” amount is typically a “statistically significant” amount,and may include an increase that is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15,20, 30 or more times (including all integers and decimal points inbetween, e.g., 1.5, 1.6, 1.7. 1.8, etc.) the amount produced by anunmodified microorganism or a differently modified microorganism.

By “obtained from” is meant that a sample such as, for example, apolynucleotide extract or polypeptide extract is isolated from, orderived from, a particular source, such as a desired organism, typicallya microorganism. “Obtained from” can also refer to the situation inwhich a polynucleotide or polypeptide sequence is isolated from, orderived from, a particular organism or microorganism. For example, apolynucleotide sequence encoding a benzaldehyde lyase enzyme may beisolated from a variety of prokaryotic or eukaryotic microorganisms,such as Pseudomonas.

The term “operably linked” as used herein means placing a gene under theregulatory control of a promoter, which then controls the transcriptionand optionally the translation of the gene. In the construction ofheterologous promoter/structural gene combinations, it is generallypreferred to position the genetic sequence or promoter at a distancefrom the gene transcription start site that is approximately the same asthe distance between that genetic sequence or promoter and the gene itcontrols in its natural setting; i.e. the gene from which the geneticsequence or promoter is derived. As is known in the art, some variationin this distance can be accommodated without loss of function.Similarly, the preferred positioning of a regulatory sequence elementwith respect to a heterologous gene to be placed under its control isdefined by the positioning of the element in its natural setting; i.e.,the genes from which it is derived. “Constitutive promoters” aretypically active, i.e., promote transcription, under most conditions.“Inducible promoters” are typically active only under certainconditions, such as in the presence of a given molecule factor (e.g.,IPTG) or a given environmental condition (e.g., CO₂ concentration,nutrient levels, light, heat). In the absence of that condition,inducible promoters typically do not allow significant or measurablelevels of transcriptional activity.

The recitation “polynucleotide” or “nucleic acid” as used hereindesignates mRNA, RNA, cRNA, rRNA, cDNA or DNA. The term typically refersto polymeric form of nucleotides of at least 10 bases in length, eitherribonucleotides or deoxynucleotides or a modified form of either type ofnucleotide. The term includes single and double stranded forms of DNA.

As will be understood by those skilled in the art, the polynucleotidesequences of this invention can include genomic sequences, extra-genomicand plasmid-encoded sequences and smaller engineered gene segments thatexpress, or may be adapted to express, proteins, polypeptides, peptidesand the like. Such segments may be naturally isolated, or modifiedsynthetically by the hand of man.

Polynucleotides may be single-stranded (coding or antisense) ordouble-stranded, and may be DNA (genomic, cDNA or synthetic) or RNAmolecules. Additional coding or non-coding sequences may, but need not,be present within a polynucleotide of the present invention, and apolynucleotide may, but need not, be linked to other molecules and/orsupport materials.

Polynucleotides may comprise a native sequence (i.e., an endogenoussequence) or may comprise a variant, or a biological functionalequivalent of such a sequence. Polynucleotide variants may contain oneor more substitutions, additions, deletions and/or insertions, asfurther described below, preferably such that the enzymatic activity ofthe encoded polypeptide is not substantially diminished relative to theunmodified polypeptide, and preferably such that the enzymatic activityof the encoded polypeptide is improved (e.g., optimized) relative to theunmodified polypeptide. The effect on the enzymatic activity of theencoded polypeptide may generally be assessed as described herein.

The polynucleotides of the present invention, regardless of the lengthof the coding sequence itself, may be combined with other DNA sequences,such as promoters, polyadenylation signals, additional restrictionenzyme sites, multiple cloning sites, other coding segments, and thelike, such that their overall length may vary considerably. It istherefore contemplated that a polynucleotide fragment of almost anylength may be employed, with the total length preferably being limitedby the ease of preparation and use in the intended recombinant DNAprotocol.

The terms “polynucleotide variant” and “variant” and the like refer topolynucleotides that display substantial sequence identity with any ofthe reference polynucleotide sequences or genes described herein, and topolynucleotides that hybridize with any polynucleotide referencesequence described herein, or any polynucleotide coding sequence of anygene or protein referred to herein, under low stringency, mediumstringency, high stringency, or very high stringency conditions that aredefined hereinafter and known in the art. These terms also encompasspolynucleotides that are distinguished from a reference polynucleotideby the addition, deletion or substitution of at least one nucleotide.Accordingly, the terms “polynucleotide variant” and “variant” includepolynucleotides in which one or more nucleotides have been added ordeleted, or replaced with different nucleotides. In this regard, it iswell understood in the art that certain alterations inclusive ofmutations, additions, deletions and substitutions can be made to areference polynucleotide whereby the altered polynucleotide retains thebiological function or activity of the reference polynucleotide, or hasincreased activity in relation to the reference polynucleotide (i.e.,optimized). Polynucleotide variants include, for example,polynucleotides having at least 50% (and at least 51% to at least 99%and all integer percentages in between) sequence identity with areference polynucleotide described herein.

The terms “polynucleotide variant” and “variant” also includenaturally-occurring allelic variants that encode these enzymes. Examplesof naturally-occurring variants include allelic variants (same locus),homologs (different locus), and orthologs (different organism).Naturally occurring variants such as these can be identified andisolated using well-known molecular biology techniques including, forexample, various polymerase chain reaction (PCR) and hybridization-basedtechniques as known in the art. Naturally occurring variants can beisolated from any organism that encodes one or more genes having asuitable enzymatic activity described herein (e.g., C—C ligase, dioldehyodrogenase, pectate lyase, alginate lyase, diol dehydratase,transporter, etc.).

Non-naturally occurring variants can be made by mutagenesis techniques,including those applied to polynucleotides, cells, or organisms. Thevariants can contain nucleotide substitutions, deletions, inversions andinsertions. Variation can occur in either or both the coding andnon-coding regions. In certain aspects, non-naturally occurring variantsmay have been optimized for use in a given microorganism (e.g., E.coli), such as by engineering and screening the enzymes for increasedactivity, stability, or any other desirable feature. The variations canproduce both conservative and non-conservative amino acid substitutions(as compared to the originally encoded product). For nucleotidesequences, conservative variants include those sequences that, becauseof the degeneracy of the genetic code, encode the amino acid sequence ofa reference polypeptide. Variant nucleotide sequences also includesynthetically derived nucleotide sequences, such as those generated, forexample, by using site-directed mutagenesis but which still encode abiologically active polypeptide. Generally, variants of a particularreference nucleotide sequence will have at least about 30%, 40% 50%,55%, 60%, 65%, 70%, generally at least about 75%, 80%, 85%, 90% to 95%or more, and even about 97% or 98% or more sequence identity to thatparticular nucleotide sequence as determined by sequence alignmentprograms described elsewhere herein using default parameters.

As used herein, the term “hybridizes under low stringency, mediumstringency, high stringency, or very high stringency conditions”describes conditions for hybridization and washing. Guidance forperforming hybridization reactions can be found in Ausubel et al.,“Current Protocols in Molecular Biology”, John Wiley & Sons Inc,1994-1998, Sections 6.3.1-6.3.6. Aqueous and non-aqueous methods aredescribed in that reference and either can be used.

Reference herein to “low stringency” conditions include and encompassfrom at least about 1% v/v to at least about 15% v/v formamide and fromat least about 1 M to at least about 2 M salt for hybridization at 42°C., and at least about 1 M to at least about 2 M salt for washing at 42°C. Low stringency conditions also may include 1% Bovine Serum Albumin(BSA), 1 mM EDTA, 0.5 M NaHPO₄ (pH 7.2), 7% SDS for hybridization at 65°C., and (i) 2×SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO₄(pH 7.2), 5% SDS for washing at room temperature. One embodiment of lowstringency conditions includes hybridization in 6× sodiumchloride/sodium citrate (SSC) at about 45° C., followed by two washes in0.2×SSC, 0.1% SDS at least at 50° C. (the temperature of the washes canbe increased to 55° C. for low stringency conditions).

“Medium stringency” conditions include and encompass from at least about16% v/v to at least about 30% v/v formamide and from at least about 0.5M to at least about 0.9 M salt for hybridization at 42° C., and at leastabout 0.1 M to at least about 0.2 M salt for washing at 55° C. Mediumstringency conditions also may include 1% Bovine Serum Albumin (BSA), 1mM EDTA, 0.5 M NaHPO₄ (pH 7.2), 7% SDS for hybridization at 65° C., and(i) 2×SSC, 0.1% SDS; or (ii) 0.5% BSA, 1 mM EDTA, 40 mM NaHPO₄ (pH 7.2),5% SDS for washing at 60-65° C. One embodiment of medium stringencyconditions includes hybridizing in 6×SSC at about 45° C., followed byone or more washes in 0.2×SSC, 0.1% SDS at 60° C.

“High stringency” conditions include and encompass from at least about31% v/v to at least about 50% v/v formamide and from about 0.01 M toabout 0.15 M salt for hybridization at 42° C., and about 0.01 M to about0.02 M salt for washing at 55° C. High stringency conditions also mayinclude 1% BSA, 1 mM EDTA, 0.5 M NaHPO₄ (pH 7.2), 7% SDS forhybridization at 65° C., and (i) 0.2×SSC, 0.1% SDS; or (ii) 0.5% BSA, 1mM EDTA, 40 mM NaHPO₄ (pH 7.2), 1% SDS for washing at a temperature inexcess of 65° C. One embodiment of high stringency conditions includeshybridizing in 6×SSC at about 45° C., followed by one or more washes in0.2×SSC, 0.1% SDS at 65° C.

One embodiment of “very high stringency” conditions includes hybridizingin 0.5 M sodium phosphate, 7% SDS at 65° C., followed by one or morewashes in 0.2×SSC, 1% SDS at 65° C.

Other stringency conditions are well known in the art and a skilledaddressee will recognize that various factors can be manipulated tooptimize the specificity of the hybridization. Optimization of thestringency of the final washes can serve to ensure a high degree ofhybridization. For detailed examples, see Ausubel et al., supra at pages2.10.1 to 2.10.16 and Sambrook et al., Current Protocols in MolecularBiology (1989), at sections 1.101 to 1.104.

While stringent washes are typically carried out at temperatures fromabout 42° C. to 68° C., one skilled in the art will appreciate thatother temperatures may be suitable for stringent conditions. Maximumhybridization rate typically occurs at about 20° C. to 25° C. below theT_(m) for formation of a DNA-DNA hybrid. It is well known in the artthat the T_(m) is the melting temperature, or temperature at which twocomplementary polynucleotide sequences dissociate. Methods forestimating T_(m) are well known in the art (see Ausubel et al., supra atpage 2.10.8).

In general, the T_(m) of a perfectly matched duplex of DNA may bepredicted as an approximation by the formula: T_(m)=81.5+16.6(log₁₀M)+0.41 (% G+C)−0.63 (% formamide)−(600/length) wherein: M is theconcentration of Na⁺, preferably in the range of 0.01 molar to 0.4molar; % G+C is the sum of guano sine and cytosine bases as a percentageof the total number of bases, within the range between 30% and 75% G+C;% formamide is the percent formamide concentration by volume; length isthe number of base pairs in the DNA duplex. The T_(m) of a duplex DNAdecreases by approximately 1° C. with every increase of 1% in the numberof randomly mismatched base pairs. Washing is generally carried out atT_(m)−15° C. for high stringency, or T_(m)−30° C. for moderatestringency.

In one example of a hybridization procedure, a membrane (e.g., anitrocellulose membrane or a nylon membrane) containing immobilized DNAis hybridized overnight at 42° C. in a hybridization buffer (50%deionizer formamide, 5×SSC, 5× Reinhardt's solution (0.1% fecal, 0.1%polyvinylpyrollidone and 0.1% bovine serum albumin), 0.1% SDS and 200mg/mL denatured salmon sperm DNA) containing a labeled probe. Themembrane is then subjected to two sequential medium stringency washes(i.e., 2×SSC, 0.1% SDS for 15 min at 45° C., followed by 2×SSC, 0.1% SDSfor 15 min at 50° C.), followed by two sequential higher stringencywashes (i.e., 0.2×SSC, 0.1% SDS for 12 min at 55° C. followed by 0.2×SSCand 0.1% SDS solution for 12 min at 65-68° C.

Polynucleotides and fusions thereof may be prepared, manipulated and/orexpressed using any of a variety of well established techniques knownand available in the art. For example, polynucleotide sequences whichencode polypeptides of the invention, or fusion proteins or functionalequivalents thereof, may be used in recombinant DNA molecules to directexpression of a selected enzyme in appropriate host cells. Due to theinherent degeneracy of the genetic code, other DNA sequences that encodesubstantially the same or a functionally equivalent amino acid sequencemay be produced and these sequences may be used to clone and express agiven polypeptide.

As will be understood by those of skill in the art, it may beadvantageous in some instances to produce polypeptide-encodingnucleotide sequences possessing non-naturally occurring codons. Forexample, codons preferred by a particular prokaryotic or eukaryotic hostcan be selected to increase the rate of protein expression or to producea recombinant RNA transcript having desirable properties, such as ahalf-life which is longer than that of a transcript generated from thenaturally occurring sequence. Such nucleotides are typically referred toas “codon-optimized.” Any of the nucleotide sequences described hereinmay be utilized in such a “codon-optimized” form. For example, thenucleotide coding sequence of the benzaldehyde lyase from Pseudomonasfluorescens may be codon-optimized for expression in E. coli.

Moreover, the polynucleotide sequences of the present invention can beengineered using methods generally known in the art in order to alterpolypeptide encoding sequences for a variety of reasons, including butnot limited to, alterations which modify the cloning, processing,expression and/or activity of the gene product.

In order to express a desired polypeptide, a nucleotide sequenceencoding the polypeptide, or a functional equivalent, may be insertedinto appropriate expression vector, i.e., a vector that contains thenecessary elements for the transcription and translation of the insertedcoding sequence. Methods which are well known to those skilled in theart may be used to construct expression vectors containing sequencesencoding a polypeptide of interest and appropriate transcriptional andtranslational control elements. These methods include in vitrorecombinant DNA techniques, synthetic techniques, and in vivo geneticrecombination. Such techniques are described in Sambrook et al.,Molecular Cloning, A Laboratory Manual (1989), and Ausubel et al.,Current Protocols in Molecular Biology (1989).

“Polypeptide,” “polypeptide fragment,” “peptide” and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues andto variants and synthetic analogues of the same. Thus, these terms applyto amino acid polymers in which one or more amino acid residues aresynthetic non-naturally occurring amino acids, such as a chemicalanalogue of a corresponding naturally occurring amino acid, as well asto naturally-occurring amino acid polymers. In certain aspects,polypeptides may include enzymatic polypeptides, or “enzymes,” whichtypically catalyze (i.e., increase the rate of) various chemicalreactions.

The recitation polypeptide “variant” refers to polypeptides that aredistinguished from a reference polypeptide sequence by the addition,deletion or substitution of at least one amino acid residue. In certainembodiments, a polypeptide variant is distinguished from a referencepolypeptide by one or more substitutions, which may be conservative ornon-conservative. In certain embodiments, the polypeptide variantcomprises conservative substitutions and, in this regard, it is wellunderstood in the art that some amino acids may be changed to otherswith broadly similar properties without changing the nature of theactivity of the polypeptide. Polypeptide variants also encompasspolypeptides in which one or more amino acids have been added ordeleted, or replaced with different amino acid residues.

The present invention contemplates the use in the methods describedherein of variants of full-length polypeptides having any of theenzymatic activities described herein, truncated fragments of thesefull-length polypeptides, variants of truncated fragments, as well astheir related biologically active fragments. Typically, biologicallyactive fragments of a polypeptide may participate in an interaction, forexample, an intra-molecular or an inter-molecular interaction. Aninter-molecular interaction can be a specific binding interaction or anenzymatic interaction (e.g., the interaction can be transient and acovalent bond is formed or broken). Biologically active fragments of apolypeptide/enzyme an enzymatic activity described herein includepeptides comprising amino acid sequences sufficiently similar to, orderived from, the amino acid sequences of a (putative) full-lengthreference polypeptide sequence. Typically, biologically active fragmentscomprise a domain or motif with at least one enzymatic activity, and mayinclude one or more (and in some cases all) of the various activedomains. A biologically active fragment of a an enzyme can be apolypeptide fragment which is, for example, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 50, 60, 70,80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 220, 240,260, 280, 300, 320, 340, 360, 380, 400, 450, 500, 600 or more contiguousamino acids, including all integers in between, of a referencepolypeptide sequence. In certain embodiments, a biologically activefragment comprises a conserved enzymatic sequence, domain, or motif, asdescribed elsewhere herein and known in the art. Suitably, thebiologically-active fragment has no less than about 1%, 10%, 25%, 50% ofan activity of the wild-type polypeptide from which it is derived.

The term “exogenous” refers generally to a polynucleotide sequence orpolypeptide that does not naturally occur in a wild-type cell ororganism, but is typically introduced into the cell by molecularbiological techniques, i.e., engineering to produce a recombinantmicroorganism. Examples of “exogenous” polynucleotides include vectors,plasmids, and/or man-made nucleic acid constructs encoding a desiredprotein or enzyme. The term “endogenous” refers generally to naturallyoccurring polynucleotide sequences or polypeptides that may be found ina given wild-type cell or organism. For example, certainnaturally-occurring bacterial or yeast species do not typically containa benzaldehyde lyase gene, and, therefore, do not comprise an“endogenous” polynucleotide sequence that encodes a benzaldehyde lyase.In this regard, it is also noted that even though an organism maycomprise an endogenous copy of a given polynucleotide sequence or gene,the introduction of a plasmid or vector encoding that sequence, such asto over-express or otherwise regulate the expression of the encodedprotein, represents an “exogenous” copy of that gene or polynucleotidesequence. Any of the of pathways, genes, or enzymes described herein mayutilize or rely on an “endogenous” sequence, or may be provided as oneor more “exogenous” polynucleotide sequences, and/or may be utilizedaccording to the endogenous sequences already contained within a givenmicroorganism.

A “recombinant” microorganism typically comprises one or more exogenousnucleotide sequences, such as in a plasmid or vector.

The recitations “sequence identity” or, for example, comprising a“sequence 50% identical to,” as used herein, refer to the extent thatsequences are identical on a nucleotide-by-nucleotide basis or an aminoacid-by-amino acid basis over a window of comparison. Thus, a“percentage of sequence identity” may be calculated by comparing twooptimally aligned sequences over the window of comparison, determiningthe number of positions at which the identical nucleic acid base (e.g.,A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser,Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn,Gln, Cys and Met) occurs in both sequences to yield the number ofmatched positions, dividing the number of matched positions by the totalnumber of positions in the window of comparison (i.e., the window size),and multiplying the result by 100 to yield the percentage of sequenceidentity.

Terms used to describe sequence relationships between two or morepolynucleotides or polypeptides include “reference sequence”,“comparison window”, “sequence identity”, “percentage of sequenceidentity” and “substantial identity”. A “reference sequence” is at least12 but frequently 15 to 18 and often at least 25 monomer units,inclusive of nucleotides and amino acid residues, in length. Because twopolynucleotides may each comprise (1) a sequence (i.e., only a portionof the complete polynucleotide sequence) that is similar between the twopolynucleotides, and (2) a sequence that is divergent between the twopolynucleotides, sequence comparisons between two (or more)polynucleotides are typically performed by comparing sequences of thetwo polynucleotides over a “comparison window” to identify and comparelocal regions of sequence similarity. A “comparison window” refers to aconceptual segment of at least 6 contiguous positions, usually about 50to about 100, more usually about 100 to about 150 in which a sequence iscompared to a reference sequence of the same number of contiguouspositions after the two sequences are optimally aligned. The comparisonwindow may comprise additions or deletions (i.e., gaps) of about 20% orless as compared to the reference sequence (which does not compriseadditions or deletions) for optimal alignment of the two sequences.Optimal alignment of sequences for aligning a comparison window may beconducted by computerized implementations of algorithms (GAP, BESTFIT,FASTA, and TFASTA in the Wisconsin Genetics Software Package Release7.0, Genetics Computer Group, 575 Science Drive Madison, Wis., USA) orby inspection and the best alignment (i.e., resulting in the highestpercentage homology over the comparison window) generated by any of thevarious methods selected. Reference also may be made to the BLAST familyof programs as for example disclosed by Altschul et al., 1997, Nucl.Acids Res. 25:3389. A detailed discussion of sequence analysis can befound in Unit 19.3 of Ausubel et al., “Current Protocols in MolecularBiology”, John Wiley & Sons Inc, 1994-1998, Chapter 15.

“Transformation” refers generally to the permanent, heritable alterationin a cell resulting from the uptake and incorporation of foreign DNAinto the host-cell genome; also, the transfer of an exogenous gene fromone organism into the genome of another organism.

By “vector” is meant a polynucleotide molecule, preferably a DNAmolecule derived, for example, from a plasmid, bacteriophage, yeast orvirus, into which a polynucleotide can be inserted or cloned. A vectorpreferably contains one or more unique restriction sites and can becapable of autonomous replication in a defined host cell including atarget cell or tissue or a progenitor cell or tissue thereof, or beintegrable with the genome of the defined host such that the clonedsequence is reproducible. Accordingly, the vector can be an autonomouslyreplicating vector, i.e., a vector that exists as an extra-chromosomalentity, the replication of which is independent of chromosomalreplication, e.g., a linear or closed circular plasmid, anextra-chromosomal element, a mini-chromosome, or an artificialchromosome. The vector can contain any means for assuringself-replication. Alternatively, the vector can be one which, whenintroduced into the host cell, is integrated into the genome andreplicated together with the chromosome(s) into which it has beenintegrated. Such a vector may comprise specific sequences that allowrecombination into a particular, desired site of the host chromosome. Avector system can comprise a single vector or plasmid, two or morevectors or plasmids, which together contain the total DNA to beintroduced into the genome of the host cell, or a transposon. The choiceof the vector will typically depend on the compatibility of the vectorwith the host cell into which the vector is to be introduced. In thepresent case, the vector is preferably one which is operably functionalin a bacterial cell, such as a cyanobacterial cell. The vector caninclude a reporter gene, such as a green fluorescent protein (GFP),which can be either fused in frame to one or more of the encodedpolypeptides, or expressed separately. The vector can also include aselection marker such as an antibiotic resistance gene that can be usedfor selection of suitable transformants.

The terms “wild-type” and “naturally occurring” are used interchangeablyto refer to a gene or gene product that has the characteristics of thatgene or gene product when isolated from a naturally occurring source. Awild type gene or gene product (e.g., a polypeptide) is that which ismost frequently observed in a population and is thus arbitrarilydesigned the “normal” or “wild-type” form of the gene.

Examples of “biomass” include aquatic or marine biomass, fruit-basedbiomass such as fruit waste, and vegetable-based biomass such asvegetable waste, among others. Examples of aquatic or marine biomassinclude, but are not limited to, kelp, giant kelp, seaweed, algae, andmarine microflora, microalgae, sea grass, and the like. In certainaspects, biomass does not include fossilized sources of carbon, such ashydrocarbons that are typically found within the top layer of theEarth's crust (e.g., natural gas, nonvolatile materials composed ofalmost pure carbon, like anthracite coal, etc).

Examples of fruit and/or vegetable biomass include, but are not limitedto, any source of pectin such as plant peel and pomace including citrus,orange, grapefruit, potato, tomato, grape, mango, gooseberry, carrot,sugar-beet, and apple, among others.

Examples of polysaccharides, oligosaccharides, monosaccharides or othersugar components of biomass include, but are not limited to, alginate,agar, carrageenan, fucoidan, pectin, gluronate, mannuronate, mannitol,lyxose, cellulose, hemicellulose, glycerol, xylitol, glucose, mannose,galactose, xylose, xylan, mannan, arabinan, arabinose, glucuronate,galacturonate (including di- and tri-galacturonates), rhamnose, and thelike.

Certain examples of alginate-derived polysaccharides include saturatedpolysaccharides, such as β-D-mannuronate, α-L-gluronate, dialginate,trialginate, pentalginate, hexylginate, heptalginate, octalginate,nonalginate, decalginate, undecalginate, dodecalginate and polyalginate,as well as unsaturated polysaccharides such as4-deoxy-L-erythro-5-hexoseulose uronic acid,4-(4-deoxy-beta-D-mann-4-enuronosyl)-D-mannuronate or L-guluronate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-dialginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-trialginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-tetralginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-pentalginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-hexylginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-heptalginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-octalginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-nonalginate,4-(4-deoxy-beta-D-mann-4-enuronosyl)-undecalginate, and4-(4-deoxy-beta-D-mann-4-enuronosyl)-dodecalginate.

Certain examples of pectin-derived polysaccharides include saturatedpolysaccharides, such as galacturonate, digalacturonate,trigalacturonate, tetragalacturonate, pentagalacturonate,hexagalacturonate, heptagalacturonate, octagalacturonate,nonagalacturonate, decagalacturonate, dodecagalacturonate,polygalacturonate, and rhamnopolygalacturonate, as well as saturatedpolysaccharides such as 4-deoxy-L-threo-5-hexosulose uronate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-galacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-digalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-trigalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-tetragalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-pentagalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-hexagalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-heptagalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-octagalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-nonagalacturonate,4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-decagalacturonate, and4-(4-Deoxy-alpha-D-gluc-4-enuronosyl)-D-dodecagalacturonate.

These polysaccharide or oligosaccharide components may be converted into“suitable monosaccharides” or other “suitable saccharides,” such as“suitable oligosaccharides,” by the microorganisms described hereinwhich are capable of growing on such polysaccharides or other sugarcomponents as a source of carbon (e.g., a sole source of carbon).

A “suitable monosaccharide” or “suitable saccharide” refers generally toany saccharide that may be produced by a recombinant microorganismgrowing on pectin, alginate, or other saccharide (e.g., galacturonate,cellulose, hemi-cellulose etc.) as a source or sole source of carbon,and also refers generally to any saccharide that may be utilized in abiofuel biosynthesis pathway of the present invention to producehydrocarbons such as biofuels or biopetrols. Examples of suitablemonosaccharides or oligosaccharides include, but are not limited to,2-keto-3-deoxy D-gluconate (KDG), D-mannitol, gluronate, mannuronate,mannitol, lyxose, glycerol, xylitol, glucose, mannose, galactose,xylose, arabinose, glucuronate, galacturonates, and rhamnose, and thelike. As noted herein, a “suitable monosaccharide” or “suitablesaccharide” as used herein may be produced by an engineered orrecombinant microorganism of the present invention, or may be obtainedfrom commercially available sources.

The recitation “commodity chemical” as used herein includes any saleableor marketable chemical that can be produced either directly or as aby-product of the methods provided herein, including biofuels and/orbiopetrols. General examples of “commodity chemicals” include, but arenot limited to, biofuels, minerals, polymer precursors, fatty alcohols,surfactants, plasticizers, and solvents. The recitation “biofuels” asused herein includes solid, liquid, or gas fuels derived, at least inpart, from a biological source, such as a recombinant microorganism.

Examples of commodity chemicals include, but are not limited to,methane, methanol, ethane, ethene, ethanol, n-propane, 1-propene,1-propanol, propanal, acetone, propionate, n-butane, 1-butene,1-butanol, butanal, butanoate, isobutanal, isobutanol, 2-methylbutanal,2-methylbutanol, 3-methylbutanal, 3-methylbutanol, 2-butene, 2-butanol,2-butanone, 2,3-butanediol, 3-hydroxy-2-butanone, 2,3-butanedione,ethylbenzene, ethenylbenzene, 2-phenylethanol, phenylacetaldehyde,1-phenylbutane, 4-phenyl-1-butene, 4-phenyl-2-butene, 1-phenyl-2-butene,1-phenyl-2-butanol, 4-phenyl-2-butanol, 1-phenyl-2-butanone,4-phenyl-2-butanone, 1-phenyl-2,3-butandiol,1-phenyl-3-hydroxy-2-butanone, 4-phenyl-3-hydroxy-2-butanone,1-phenyl-2,3-butanedione, n-pentane, ethylphenol, ethenylphenol,2-(4-hydroxyphenyl)ethanol, 4-hydroxyphenylacetaldehyde,1-(4-hydroxyphenyl) butane, 4-(4-hydroxyphenyl)-1-butene,4-(4-hydroxyphenyl)-2-butene, 1-(4-hydroxyphenyl)-1-butene,1-(4-hydroxyphenyl)-2-butanol, 4-(4-hydroxyphenyl)-2-butanol,1-(4-hydroxyphenyl)-2-butanone, 4-(4-hydroxyphenyl)-2-butanone,1-(4-hydroxyphenyl)-2,3-butandiol,1-(4-hydroxyphenyl)-3-hydroxy-2-butanone,4-(4-hydroxyphenyl)-3-hydroxy-2-butanone,1-(4-hydroxyphenyl)-2,3-butanonedione, indolylethane, indolylethene,2-(indole-3-)ethanol, n-pentane, 1-pentene, 1-pentanol, pentanal,pentanoate, 2-pentene, 2-pentanol, 3-pentanol, 2-pentanone, 3-pentanone,4-methylpentanal, 4-methylpentanol, 2,3-pentanediol,2-hydroxy-3-pentanone, 3-hydroxy-2-pentanone, 2,3-pentanedione,2-methylpentane, 4-methyl-1-pentene, 4-methyl-2-pentene,4-methyl-3-pentene, 4-methyl-2-pentanol, 2-methyl-3-pentanol,4-methyl-2-pentanone, 2-methyl-3-pentanone, 4-methyl-2,3-pentanediol,4-methyl-2-hydroxy-3-pentanone, 4-methyl-3-hydroxy-2-pentanone,4-methyl-2,3-pentanedione, 1-phenylpentane, 1-phenyl-1-pentene,1-phenyl-2-pentene, 1-phenyl-3-pentene, 1-phenyl-2-pentanol,1-phenyl-3-pentanol, 1-phenyl-2-pentanone, 1-phenyl-3-pentanone,1-phenyl-2,3-pentanediol, 1-phenyl-2-hydroxy-3-pentanone,1-phenyl-3-hydroxy-2-pentanone, 1-phenyl-2,3-pentanedione,4-methyl-1-phenylpentane, 4-methyl-1-phenyl-1-pentene,4-methyl-1-phenyl-2-pentene, 4-methyl-1-phenyl-3-pentene,4-methyl-1-phenyl-3-pentanol, 4-methyl-1-phenyl-2-pentanol,4-methyl-1-phenyl-3-pentanone, 4-methyl-1-phenyl-2-pentanone,4-methyl-1-phenyl-2,3-pentanediol, 4-methyl-1-phenyl-2,3-pentanedione,4-methyl-1-phenyl-3-hydroxy-2-pentanone,4-methyl-1-phenyl-2-hydroxy-3-pentanone, 1-(4-hydroxyphenyl) pentane,1-(4-hydroxyphenyl)-1-pentene, 1-(4-hydroxyphenyl)-2-pentene,1-(4-hydroxyphenyl)-3-pentene, 1-(4-hydroxyphenyl)-2-pentanol,1-(4-hydroxyphenyl)-3-pentanol, 1-(4-hydroxyphenyl)-2-pentanone,1-(4-hydroxyphenyl)-3-pentanone, 1-(4-hydroxyphenyl)-2,3-pentanediol,1-(4-hydroxyphenyl)-2-hydroxy-3-pentanone,1-(4-hydroxyphenyl)-3-hydroxy-2-pentanone,1-(4-hydroxyphenyl)-2,3-pentanedione, 4-methyl-1-(4-hydroxyphenyl)pentane, 4-methyl-1-(4-hydroxyphenyl)-2-pentene,4-methyl-1-(4-hydroxyphenyl)-3-pentene,4-methyl-1-(4-hydroxyphenyl)-1-pentene,4-methyl-1-(4-hydroxyphenyl)-3-pentanol,4-methyl-1-(4-hydroxyphenyl)-2-pentanol,4-methyl-1-(4-hydroxyphenyl)-3-pentanone,4-methyl-1-(4-hydroxyphenyl)-2-pentanone,4-methyl-1-(4-hydroxyphenyl)-2,3-pentanediol,4-methyl-1-(4-hydroxyphenyl)-2,3-pentanedione,4-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-pentanone,4-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-pentanone, 1-indole-3-pentane,1-(indole-3)-1-pentene, 1-(indole-3)-2-pentene, 1-(indole-3)-3-pentene,1-(indole-3)-2-pentanol, 1-(indole-3)-3-pentanol,1-(indole-3)-2-pentanone, 1-(indole-3)-3-pentanone,1-(indole-3)-2,3-pentanediol, 1-(indole-3)-2-hydroxy-3-pentanone,1-(indole-3)-3-hydroxy-2-pentanone, 1-(indole-3)-2,3-pentanedione,4-methyl-1-(indole-3-)pentane, 4-methyl-1-(indole-3)-2-pentene,4-methyl-1-(indole-3)-3-pentene, 4-methyl-1-(indole-3)-1-pentene,4-methyl-2-(indole-3)-3-pentanol, 4-methyl-1-(indole-3)-2-pentanol,4-methyl-1-(indole-3)-3-pentanone, 4-methyl-1-(indole-3)-2-pentanone,4-methyl-1-(indole-3)-2,3-pentanediol,4-methyl-1-(indole-3)-2,3-pentanedione,4-methyl-1-(indole-3)-3-hydroxy-2-pentanone,4-methyl-1-(indole-3)-2-hydroxy-3-pentanone, n-hexane, 1-hexene,1-hexanol, hexanal, hexanoate, 2-hexene, 3-hexene, 2-hexanol, 3-hexanol,2-hexanone, 3-hexanone, 2,3-hexanediol, 2,3-hexanedione, 3,4-hexanediol,3,4-hexanedione, 2-hydroxy-3-hexanone, 3-hydroxy-2-hexanone,3-hydroxy-4-hexanone, 4-hydroxy-3-hexanone, 2-methylhexane,3-methylhexane, 2-methyl-2-hexene, 2-methyl-3-hexene, 5-methyl-1-hexene,5-methyl-2-hexene, 4-methyl-1-hexene, 4-methyl-2-hexene,3-methyl-3-hexene, 3-methyl-2-hexene, 3-methyl-1-hexene,2-methyl-3-hexanol, 5-methyl-2-hexanol, 5-methyl-3-hexanol,2-methyl-3-hexanone, 5-methyl-2-hexanone, 5-methyl-3-hexanone,2-methyl-3,4-hexanediol, 2-methyl-3,4-hexanedione,5-methyl-2,3-hexanediol, 5-methyl-2,3-hexanedione,4-methyl-2,3-hexanediol, 4-methyl-2,3-hexanedione,2-methyl-3-hydroxy-4-hexanone, 2-methyl-4-hydroxy-3-hexanone,5-methyl-2-hydroxy-3-hexanone, 5-methyl-3-hydroxy-2-hexanone,4-methyl-2-hydroxy-3-hexanone, 4-methyl-3-hydroxy-2-hexanone,2,5-dimethylhexane, 2,5-dimethyl-2-hexene, 2,5-dimethyl-3-hexene,2,5-dimethyl-3-hexanol, 2,5-dimethyl-3-hexanone,2,5-dimethyl-3,4-hexanediol, 2,5-dimethyl-3,4-hexanedione,2,5-dimethyl-3-hydroxy-4-hexanone, 5-methyl-1-phenylhexane,4-methyl-1-phenylhexane, 5-methyl-1-phenyl-1-hexene,5-methyl-1-phenyl-2-hexene, 5-methyl-1-phenyl-3-hexene,4-methyl-1-phenyl-1-hexene, 4-methyl-1-phenyl-2-hexene,4-methyl-1-phenyl-3-hexene, 5-methyl-1-phenyl-2-hexanol,5-methyl-1-phenyl-3-hexanol, 4-methyl-1-phenyl-2-hexanol,4-methyl-1-phenyl-3-hexanol, 5-methyl-1-phenyl-2-hexanone,5-methyl-1-phenyl-3-hexanone, 4-methyl-1-phenyl-2-hexanone,4-methyl-1-phenyl-3-hexanone, 5-methyl-1-phenyl-2,3-hexanediol,4-methyl-1-phenyl-2,3-hexanediol,5-methyl-1-phenyl-3-hydroxy-2-hexanone,5-methyl-1-phenyl-2-hydroxy-3-hexanone,4-methyl-1-phenyl-3-hydroxy-2-hexanone,4-methyl-1-phenyl-2-hydroxy-3-hexanone,5-methyl-1-phenyl-2,3-hexanedione, 4-methyl-1-phenyl-2,3-hexanedione,4-methyl-1-(4-hydroxyphenyl)hexane,5-methyl-1-(4-hydroxyphenyl)-1-hexene,5-methyl-1-(4-hydroxyphenyl)-2-hexene,5-methyl-1-(4-hydroxyphenyl)-3-hexene,4-methyl-1-(4-hydroxyphenyl)-1-hexene,4-methyl-1-(4-hydroxyphenyl)-2-hexene,4-methyl-1-(4-hydroxyphenyl)-3-hexene,5-methyl-1-(4-hydroxyphenyl)-2-hexanol,5-methyl-1-(4-hydroxyphenyl)-3-hexanol,4-methyl-1-(4-hydroxyphenyl)-2-hexanol,4-methyl-1-(4-hydroxyphenyl)-3-hexanol,5-methyl-1-(4-hydroxyphenyl)-2-hexanone,5-methyl-1-(4-hydroxyphenyl)-3-hexanone,4-methyl-1-(4-hydroxyphenyl)-2-hexanone,4-methyl-1-(4-hydroxyphenyl)-3-hexanone,5-methyl-1-(4-hydroxyphenyl)-2,3-hexanediol,4-methyl-1-(4-hydroxyphenyl)-2,3-hexanediol,5-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-hexanone,5-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-hexanone,4-methyl-1-(4-hydroxyphenyl)-3-hydroxy-2-hexanone,4-methyl-1-(4-hydroxyphenyl)-2-hydroxy-3-hexanone,5-methyl-1-(4-hydroxyphenyl)-2,3-hexanedione,4-methyl-1-(4-hydroxyphenyl)-2,3-hexanedione,4-methyl-1-(indole-3-)hexane, 5-methyl-1-(indole-3)-1-hexene,5-methyl-1-(indole-3)-2-hexene, 5-methyl-1-(indole-3)-3-hexene,4-methyl-1-(indole-3)-1-hexene, 4-methyl-1-(indole-3)-2-hexene,4-methyl-1-(indole-3)-3-hexene, 5-methyl-1-(indole-3)-2-hexanol,5-methyl-1-(indole-3)-3-hexanol, 4-methyl-1-(indole-3)-2-hexanol,4-methyl-1-(indole-3)-3-hexanol, 5-methyl-1-(indole-3)-2-hexanone,5-methyl-1-(indole-3)-3-hexanone, 4-methyl-1-(indole-3)-2-hexanone,4-methyl-1-(indole-3)-3-hexanone, 5-methyl-1-(indole-3)-2,3-hexanediol,4-methyl-1-(indole-3)-2,3-hexanediol,5-methyl-1-(indole-3)-3-hydroxy-2-hexanone,5-methyl-1-(indole-3)-2-hydroxy-3-hexanone,4-methyl-1-(indole-3)-3-hydroxy-2-hexanone,4-methyl-1-(indole-3)-2-hydroxy-3-hexanone,5-methyl-1-(indole-3)-2,3-hexanedione,4-methyl-1-(indole-3)-2,3-hexanedione, n-heptane, 1-heptene, 1-heptanol,heptanal, heptanoate, 2-heptene, 3-heptene, 2-heptanol, 3-heptanol,4-heptanol, 2-heptanone, 3-heptanone, 4-heptanone, 2,3-heptanediol,2,3-heptanedione, 3,4-heptanediol, 3,4-heptanedione,2-hydroxy-3-heptanone, 3-hydroxy-2-heptanone, 3-hydroxy-4-heptanone,4-hydroxy-3-heptanone, 2-methylheptane, 3-methylheptane,6-methyl-2-heptene, 6-methyl-3-heptene, 2-methyl-3-heptene,2-methyl-2-heptene, 5-methyl-2-heptene, 5-methyl-3-heptene,3-methyl-3-heptene, 2-methyl-3-heptanol, 2-methyl-4-heptanol,6-methyl-3-heptanol, 5-methyl-3-heptanol, 3-methyl-4-heptanol,2-methyl-3-heptanone, 2-methyl-4-heptanone, 6-methyl-3-heptanone,5-methyl-3-heptanone, 3-methyl-4-heptanone, 2-methyl-3,4-heptanediol,2-methyl-3,4-heptanedione, 6-methyl-3,4-heptanediol,6-methyl-3,4-heptanedione, 5-methyl-3,4-heptanediol,5-methyl-3,4-heptanedione, 2-methyl-3-hydroxy-4-heptanone,2-methyl-4-hydroxy-3-heptanone, 6-methyl-3-hydroxy-4-heptanone,6-methyl-4-hydroxy-3-heptanone, 5-methyl-3-hydroxy-4-heptanone,5-methyl-4-hydroxy-3-heptanone, 2,6-dimethylheptane,2,5-dimethylheptane, 2,6-dimethyl-2-heptene, 2,6-dimethyl-3-heptene,2,5-dimethyl-2-heptene, 2,5-dimethyl-3-heptene, 3,6-dimethyl-3-heptene,2,6-dimethyl-3-heptanol, 2,6-dimethyl-4-heptanol,2,5-dimethyl-3-heptanol, 2,5-dimethyl-4-heptanol,2,6-dimethyl-3,4-heptanediol, 2,6-dimethyl-3,4-heptanedione,2,5-dimethyl-3,4-heptanediol, 2,5-dimethyl-3,4-heptanedione,2,6-dimethyl-3-hydroxy-4-heptanone, 2,6-dimethyl-4-hydroxy-3-heptanone,2,5-dimethyl-3-hydroxy-4-heptanone, 2,5-dimethyl-4-hydroxy-3-heptanone,n-octane, 1-octene, 2-octene, 1-octanol, octanal, octanoate, 3-octene,4-octene, 4-octanol, 4-octanone, 4,5-octanediol, 4,5-octanedione,4-hydroxy-5-octanone, 2-methyloctane, 2-methyl-3-octene,2-methyl-4-octene, 7-methyl-3-octene, 3-methyl-3-octene,3-methyl-4-octene, 6-methyl-3-octene, 2-methyl-4-octanol,7-methyl-4-octanol, 3-methyl-4-octanol, 6-methyl-4-octanol,2-methyl-4-octanone, 7-methyl-4-octanone, 3-methyl-4-octanone,6-methyl-4-octanone, 2-methyl-4,5-octanediol, 2-methyl-4,5-octanedione,3-methyl-4,5-octanediol, 3-methyl-4,5-octanedione,2-methyl-4-hydroxy-5-octanone, 2-methyl-5-hydroxy-4-octanone,3-methyl-4-hydroxy-5-octanone, 3-methyl-5-hydroxy-4-octanone,2,7-dimethyloctane, 2,7-dimethyl-3-octene, 2,7-dimethyl-4-octene,2,7-dimethyl-4-octanol, 2,7-dimethyl-4-octanone,2,7-dimethyl-4,5-octanediol, 2,7-dimethyl-4,5-octanedione,2,7-dimethyl-4-hydroxy-5-octanone, 2,6-dimethyloctane,2,6-dimethyl-3-octene, 2,6-dimethyl-4-octene, 3,7-dimethyl-3-octene,2,6-dimethyl-4-octanol, 3,7-dimethyl-4-octanol, 2,6-dimethyl-4-octanone,3,7-dimethyl-4-octanone, 2,6-dimethyl-4,5-octanediol,2,6-dimethyl-4,5-octanedione, 2,6-dimethyl-4-hydroxy-5-octanone,2,6-dimethyl-5-hydroxy-4-octanone, 3,6-dimethyloctane,3,6-dimethyl-3-octene, 3,6-dimethyl-4-octene, 3,6-dimethyl-4-octanol,3,6-dimethyl-4-octanone, 3,6-dimethyl-4,5-octanediol,3,6-dimethyl-4,5-octanedione, 3,6-dimethyl-4-hydroxy-5-octanone,n-nonane, 1-nonene, 1-nonanol, nonanal, nonanoate, 2-methylnonane,2-methyl-4-nonene, 2-methyl-5-nonene, 8-methyl-4-nonene,2-methyl-5-nonanol, 8-methyl-4-nonanol, 2-methyl-5-nonanone,8-methyl-4-nonanone, 8-methyl-4,5-nonanediol, 8-methyl-4,5-nonanedione,8-methyl-4-hydroxy-5-nonanone, 8-methyl-5-hydroxy-4-nonanone,2,8-dimethylnonane, 2,8-dimethyl-3-nonene, 2,8-dimethyl-4-nonene,2,8-dimethyl-5-nonene, 2,8-dimethyl-4-nonanol, 2,8-dimethyl-5-nonanol,2,8-dimethyl-4-nonanone, 2,8-dimethyl-5-nonanone,2,8-dimethyl-4,5-nonanediol, 2,8-dimethyl-4,5-nonanedione,2,8-dimethyl-4-hydroxy-5-nonanone, 2,8-dimethyl-5-hydroxy-4-nonanone,2,7-dimethylnonane, 3,8-dimethyl-3-nonene, 3,8-dimethyl-4-nonene,3,8-dimethyl-5-nonene, 3,8-dimethyl-4-nonanol, 3,8-dimethyl-5-nonanol,3,8-dimethyl-4-nonanone, 3,8-dimethyl-5-nonanone,3,8-dimethyl-4,5-nonanediol, 3,8-dimethyl-4,5-nonanedione,3,8-dimethyl-4-hydroxy-5-nonanone, 3,8-dimethyl-5-hydroxy-4-nonanone,n-decane, 1-decene, 1-decanol, decanoate, 2,9-dimethyldecane,2,9-dimethyl-3-decene, 2,9-dimethyl-4-decene, 2,9-dimethyl-5-decanol,2,9-dimethyl-5-decanone, 2,9-dimethyl-5,6-decanediol,2,9-dimethyl-6-hydroxy-5-decanone,2,9-dimethyl-5,6-decanedionen-undecane, 1-undecene, 1-undecanol,undecanal. undecanoate, n-dodecane, 1-dodecene, 1-dodecanol, dodecanal,dodecanoate, n-dodecane, 1-decadecene, 1-dodecanol, ddodecanal,dodecanoate, n-tridecane, 1-tridecene, 1-tridecanol, tridecanal,tridecanoate, n-tetradecane, 1-tetradecene, 1-tetradecanol,tetradecanal, tetradecanoate, n-pentadecane, 1-pentadecene,1-pentadecanol, pentadecanal, pentadecanoate, n-hexadecane,1-hexadecene, 1-hexadecanol, hexadecanal, hexadecanoate, n-heptadecane,1-heptadecene, 1-heptadecanol, heptadecanal, heptadecanoate,n-octadecane, 1-octadecene, 1-octadecanol, octadecanal, octadecanoate,n-nonadecane, 1-nonadecene, 1-nonadecanol, nonadecanal, nonadecanoate,eicosane, 1-eicosene, 1-eicosanol, eicosanal, eicosanoate, 3-hydroxypropanal, 1,3-propanediol, 4-hydroxybutanal, 1,4-butanediol,3-hydrxy-2-butanone, 2,3-butandiol, 1,5-pentane diol, homocitrate,homoisocitorate, b-hydroxy adipate, glutarate, glutarsemialdehyde,glutaraldehyde, 2-hydroxy-1-cyclopentanone, 1,2-cyclopentanediol,cyclopentanone, cyclopentanol, (S)-2-acetolactate,(R)-2,3-Dihydroxy-isovalerate, 2-oxoisovalerate, isobutyryl-CoA,isobutyrate, isobutyraldehyde, 5-amino pentaldehyde, 1,10-diaminodecane,1,10-diamino-5-decene, 1,10-diamino-5-hydroxydecane,1,10-diamino-5-decanone, 1,10-diamino-5,6-decanediol,1,10-diamino-6-hydroxy-5-decanone, phenylacetoaldehyde,1,4-diphenylbutane, 1,4-diphenyl-1-butene, 1,4-diphenyl-2-butene,1,4-diphenyl-2-butanol, 1,4-diphenyl-2-butanone,1,4-diphenyl-2,3-butanediol, 1,4-diphenyl-3-hydroxy-2-butanone,1-(4-hydeoxyphenyl)-4-phenylbutane,1-(4-hydeoxyphenyl)-4-phenyl-1-butene,1-(4-hydeoxyphenyl)-4-phenyl-2-butene,1-(4-hydeoxyphenyl)-4-phenyl-2-butanol,1-(4-hydeoxyphenyl)-4-phenyl-2-butanone,1-(4-hydeoxyphenyl)-4-phenyl-2,3-butanediol,1-(4-hydeoxyphenyl)-4-phenyl-3-hydroxy-2-butanone,1-(indole-3)-4-phenylbutane, 1-(indole-3)-4-phenyl-1-butene,1-(indole-3)-4-phenyl-2-butene, 1-(indole-3)-4-phenyl-2-butanol,1-(indole-3)-4-phenyl-2-butanone, 1-(indole-3)-4-phenyl-2,3-butanediol,1-(indole-3)-4-phenyl-3-hydroxy-2-butanone,4-hydroxyphenylacetoaldehyde, 1,4-di(4-hydroxyphenyl)butane,1,4-di(4-hydroxyphenyl)-1-butene, 1,4-di(4-hydroxyphenyl)-2-butene,1,4-di(4-hydroxyphenyl)-2-butanol, 1,4-di(4-hydroxyphenyl)-2-butanone,1,4-di(4-hydroxyphenyl)-2,3-butanediol,1,4-di(4-hydroxyphenyl)-3-hydroxy-2-butanone,1-(4-hydroxyphenyl)-4-(indole-3-)butane,1-(4-hydroxyphenyl)-4-(indole-3)-1-butene,1-di(4-hydroxyphenyl)-4-(indole-3)-2-butene,1-(4-hydroxyphenyl)-4-(indole-3)-2-butanol,1-(4-hydroxyphenyl)-4-(indole-3)-2-butanone,1-(4-hydroxyphenyl)-4-(indole-3)-2,3-butanediol,1-(4-hydroxyphenyl-4-(indole-3)-3-hydroxy-2-butanone,indole-3-acetoaldehyde, 1,4-di(indole-3-)butane,1,4-di(indole-3)-1-butene, 1,4-di(indole-3)-2-butene,1,4-di(indole-3)-2-butanol, 1,4-di(indole-3)-2-butanone,1,4-di(indole-3)-2,3-butanediol, 1,4-di(indole-3)-3-hydroxy-2-butanone,succinate semialdehyde, hexane-1,8-dicarboxylic acid,3-hexene-1,8-dicarboxylic acid, 3-hydroxy-hexane-1,8-dicarboxylic acid,3-hexanone-1,8-dicarboxylic acid, 3,4-hexanediol-1,8-dicarboxylic acid,4-hydroxy-3-hexanone-1,8-dicarboxylic acid, fucoidan, iodine,chlorophyll, carotenoid, calcium, magnesium, iron, sodium, potassium,phosphate, and the like.

The recitation “optimized” as used herein refers to a pathway, gene,polypeptide, enzyme, or other molecule having an altered biologicalactivity, such as by the genetic alteration of a polypeptide's aminoacid sequence or by the alteration/modification of the polypeptide'ssurrounding cellular environment, to improve its functionalcharacteristics in relation to the original molecule or originalcellular environment (e.g., a wild-type sequence of a given polypeptideor a wild-type microorganism). Any of the polypeptides or enzymesdescribed herein may be optionally “optimized,” and any of the genes ornucleotide sequences described herein may optionally encode an optimizedpolypeptide or enzyme. Any of the pathways described herein mayoptionally contain one or more “optimized” enzymes, or one or morenucleotide sequences encoding for an optimized enzyme or polypeptide.

Typically, the improved functional characteristics of the polypeptide,enzyme, or other molecule relate to the suitability of the polypeptideor other molecule for use in a biological pathway (e.g., a biosynthesispathway, a C—C ligation pathway) to convert a monosaccharide oroligosaccharide into a biofuel. Certain embodiments, therefore,contemplate the use of “optimized” biological pathways. An exemplary“optimized” polypeptide may contain one or more alterations or mutationsin its amino acid coding sequence (e.g., point mutations, deletions,addition of heterologous sequences) that facilitate improved expressionand/or stability in a given microbial system or microorganism, allowregulation of polypeptide activity in relation to a desired substrate(e.g., inducible or repressible activity), modulate the localization ofthe polypeptide within a cell (e.g., intracellular localization,extracellular secretion), and/or effect the polypeptide's overall levelof activity in relation to a desired substrate (e.g., reduce or increaseenzymatic activity). A polypeptide or other molecule may also be“optimized” for use with a given microbial system or microorganism byaltering one or more pathways within that system or organism, such as byaltering a pathway that regulates the expression (e.g., up-regulation),localization, and/or activity of the “optimized” polypeptide or othermolecule, or by altering a pathway that minimizes the production ofundesirable by-products, among other alterations. In this manner, apolypeptide or other molecule may be “optimized” with or withoutaltering its wild-type amino acid sequence or original chemicalstructure. Optimized polypeptides or biological pathways may beobtained, for example, by direct mutagenesis or by natural selection fora desired phenotype, according to techniques known in the art.

In certain aspects, “optimized” genes or polypeptides may comprise anucleotide coding sequence or amino acid sequence that is 50% to 99%identical (including all integeres in between) to the nucleotide oramino acid sequence of a reference (e.g., wild-type) gene orpolypeptide. In certain aspects, an “optimized” polypeptide or enzymemay have about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100(including all integers and decimal points in between e.g., 1.2, 1.3,1.4, 1.5, 5.5, 5.6, 5.7, 60, 70, etc.), or more times the biologicalactivity of a reference polypeptide.

Certain aspects of the invention also include a commodity chemical, suchas a biofuel, that is produced according to the methods and recombinantmicroorganisms described herein. Such a biofuel (e.g., medium to longchain alkane) may be distinguished from other fuels, such as those fuelsproduced by traditional refinery from crude carbon sources, byradio-carbon dating techniques. For instance, carbon has two stable,nonradioactive isotopes: carbon-12 (¹²C), and carbon-13 (¹³C). Inaddition, there are trace amounts of the unstable isotope carbon-14(¹⁴C) on Earth. Carbon-14 has a half-life of 5730 years, and would havelong ago vanished from Earth were it not for the unremitting impact ofcosmic rays on nitrogen in the Earth's atmosphere, which create more ofthis isotope. The neutrons resulting from the cosmic ray interactionsparticipate in the following nuclear reaction on the atoms of nitrogenmolecules (N₂) in the atmospheric air:

n +  ₇¹⁴N →  ₆¹⁴C + p

Plants and other photosynthetic organisms take up atmospheric carbondioxide by photosynthesis. Since many plants are ingested by animals,every living organism on Earth is constantly exchanging carbon-14 withits environment for the duration of its existence. Once an organismdies, however, this exchange stops, and the amount of carbon-14gradually decreases over time through radioactive beta decay.

Most hydrocarbon-based fuels, such as crude oil and natural gas derivedfrom mining operations, are the result of compression and heating ofancient organic materials (i.e., kerogen) over geological time.Formation of petroleum typically occurs from hydrocarbon pyrolysis, in avariety of mostly endothermic reactions at high temperature and/orpressure. Today's oil formed from the preserved remains of prehistoriczooplankton and algae, which had settled to a sea or lake bottom inlarge quantities under anoxic conditions (the remains of prehistoricterrestrial plants, on the other hand, tended to form coal). Overgeological time the organic matter mixed with mud, and was buried underheavy layers of sediment resulting in high levels of heat and pressure(known as diagenesis). This process caused the organic matter tochemically change, first into a waxy material known as kerogen which isfound in various oil shales around the world, and then with more heatinto liquid and gaseous hydrocarbons in a process known as catagenesis.Most hydrocarbon based fuels derived from crude oil have been undergoinga process of carbon-14 decay over geological time, and, thus, will havelittle to no detectable carbon-14. In contrast, certain biofuelsproduced by the living microorganisms of the present invention willcomprise carbon-14 at a level comparable to all other presently livingthings (i.e., an equilibrium level). In this manner, by measuring thecarbon-12 to carbon-14 ratio of a hydrocarbon-based biofuel of thepresent invention, and comparing that ratio to a hydrocarbon based fuelderived from crude oil, the biofuels produced by the methods providedherein can be structurally distinguished from typical sources ofhydrocarbon based fuels.

Embodiments of the present invention include methods for converting apolysaccharide to a suitable monosaccharide comprising, (a) obtainingthe polysaccharide; and (b) contacting the polysaccharide with arecombinant microorganism or microbial system comprising such amicroorganism for a time sufficient to convert the polysaccharide to asuitable monosaccharide, wherein the microbial system comprises, (i) atleast one gene encoding and expressing an enzyme selected from a lyaseand a hydrolase, wherein the lyase and/or hydrolase optionally comprisesat least one signal peptide or at least one autotransporter domain; (ii)at least one gene encoding and expressing an enzyme selected from amonosaccharide transporter, a disaccharide transporter, a trisaccharidetransporter, an oligosaccharide transporter, and a polysaccharidetransporter; and (iii) at least one gene encoding and expressing anenzyme selected from a monosaccharide dehydrogenase, an isomerase, adehydratase, a kinase, and an aldolase, thereby converting thepolysaccharide to a suitable monosaccharide.

Alternatively, certain aspects may include methods for converting apolysaccharide to a suitable monosaccharide comprising, (a) obtainingthe polysaccharide; and (b) contacting the polysaccharide with amicrobial system for a time sufficient to convert the polysaccharide toa suitable monosaccharide, wherein the microbial system comprises, (i)at least one gene encoding and expressing an enzyme selected from alyase and a hydrolase; (ii) at least one gene encoding and expressing asuperchannel; and (iii) at least one gene encoding and expressing anenzyme selected from a monosaccharide dehydrogenase, an isomerase, adehydratase, a kinase, and an aldolase, thereby converting thepolysaccharide to a suitable monosaccharide.

In certain embodiments, a microbial system or isolated microorganism iscapable of growing using a polysaccharide (e.g., alginate, pectin, etc.)as a sole source of carbon and/or energy. A “sole source of carbon”refers generally to the ability to grow on a given carbon source as theonly carbon source in a given growth medium.

With regard to alginate, approximately 50 percent of seaweed dry-weightcomprises various sugar components, among which alginate and mannitolare major components corresponding to 30 and 15 percent of seaweeddry-weight, respectively. With regard to pectin, although microorganismssuch as E. coli are generally considered as a host organisms insynthetic biology, and although such microorganism are able tometabolize mannitol, they completely lack the ability to degrade andmetabolize alginate. In this regard, many laboratory or wild-typemicroorganisms, such as E. coli, are unable to grow on alginate as asole source of carbon. Similarly, many organisms such as E. coli areunable to degrade and metabolize pectin, a polysaccharide found in manyfood waste products, and, thus are unable to grown on pectin as a solesource of carbon. Accordingly, embodiments of the present applicationinclude engineered microorganisms, such as E. coli, or microbial systemscontaining such engineered microorganisms, that are capable of usingpolysaccharides, such as alginate and pectin, as a sole source of carbonand/or energy.

Alginate is a block co-polymer of β-D-mannuronate (M) and α-D-gluronate(G) (M and G are epimeric about the C5-carboxyl group). Each alginatepolymer comprises regions of all M (polyM), all G (polyG), and/or themixture of M and G (polyMG). To utilize alginate to produce one or moresuitable monosaccharides, certain aspects of the present inventionprovide an engineered or recombinant microorganism or microbial systemthat is able to degrade or de-polymerize alginate and to use it as asource of carbon and/or energy. As one means of accomplishing thispurpose, such recombinant microorganisms may incorporate a set ofpolysaccharide degrading or depolymerizing enzymes such as alginatelyases (ALs) to the microbial system.

ALs are mainly classified into two distinctive subfamilies depending ontheir acts of catalysis: endo-(EC 4.2.2.3) and exo-acting (EC 4.2.2.-)ALs. Endo-acting ALs are further classified based on their catalyticspecificity; M specific and G specific ALs. The endo-acting ALs randomlycleave alginate via a 1-elimination mechanism and mainly depolymerizealginate to di-, tri- and tetrasaccharides. The uronate at thenon-reducing terminus of each oligosaccharide are converted tounsaturated sugar uronate, 4-deoxy-α-L-erythro-hex-4-ene pyranosyluronates. The exo-acting ALs catalyze further depolymerization of theseoligosaccharides and release unsaturated monosaccharides, which may benon-enzymatically converted to monosaccharides, including α-keto acid,4-deoxy-α-L-erythro-hexoselulose uronate (DEHU). Certain embodiments ofan engineered microbial system or isolated, engineered microorganism mayinclude endoM-, endoG- and exo-acting ALs to degrade or depolymerizeaquatic or marine-biomass polysaccharides such as alginate to amonosaccharide such as DEHU.

Embodiments of the present invention may also include lyases such asalginate lyases isolated from various sources, including, but notlimited to, marine algae, mollusks, and wide varieties of microbes suchas genus Pseudomonas, Vibrio, and Sphingomonas. Many alginate lyases areendo-acting M specific, several are G specific, and few are exo-acting.For example, ALs isolated from Sphingomonas sp. strain Al include fiveendo-acting ALs, Al-I, Al-II, Al-II′, Al-III, and Al-IV′ and anexo-acting AL, Al-IV.

Typically, Al-I, Al-II, and Al-III have molecular weights of 66 kDa, 25kDa, and 40 kDa, respectively. AI-II and AI-III are self-splicingproducts of Al-1. AI-II may be more specific to G and Al-III may bespecific to M. Al-I may have high activity for both M and G. Al-IV hasmolecular weight of about 85 kDa and catalyzes exo-lyticdepolymerization of oligoalginate. Although both Al-II′ and Al-IV′ arefunctional homologues of Al-II and Al-IV. AI-II′ has endo-lytic activityand may have no preference to M or G. Al-IV has primarily endo-lyticactivity. In addition to these ALs, exo-lytic AL Atu3025 derived fromAgrobacterium tumefaciens has high activity for depolymerization ofoligoalginate, and may be used in certain embodiments of the presentinvention. Certain embodiments may incorporate into the microbial systemor isolated microorganism the genes encoding Al-I, Al-II′, Al-IV, andAtu3025, and may include optimal codon usage for the suitable hostorganisms, such as E. coli.

Certain examples of alginate lyases or oligoalginate lyases that may beutilized herein include enzymes or polypeptides sharing at least 60%,70%, 80%, 90%, 95%, 98%, or more sequence identity (including allintegers in between) to SEQ ID NOS:67-68, which show the nucleotide (SEQID NO:67) and polyeptide (SEQ ID NO:68) sequences of oligoalginate lyaseAtu3025 isolated from Agrobacterium tumefaciens. Certain examples ofalginate lyases that may be utilized herein include enzymes orpolypeptides sharing at least 60%, 70%, 80%, 90%, 95%, 98%, or moresequence identity (including all integers in between) to the alginatelyase enyzmes described in FIG. 37, as well as the secreted alginatelyase encoded by Vs24254 from Vibrio splendidus.

In certain embodiments, a microbial system or recombinant microorganismmay be engineered to secrete or display the lyases or alginate lyases(ALs) to the culture media, such as by incorporating a signal peptide orautotransporter domain into the lyase. In this regard, it is typicallyunderstood that bacteria have at least four different types of proteinsecretion machinery (type I, II, III and IV). For example, in E. coli,the type II secretion machinery is used for the secretion of recombinantproteins. The type II secretion machinery may comprise a two-stepprocess: the translocation of premature proteins tagged with signalpeptides to the periplasm fraction and processing to the mature proteinsfollowed by secretion to media.

The first process may proceed by any of three different pathways:secB-dependent pathway, signal recognition particle (SRP) pathway, ortwin-arginine translocation (TAT) pathway. Recombinant proteins may besecreted into periplasm fraction. The fates of the mature proteins varydependent on the type of proteins. For example, some proteins aresecreted spontaneously by diffusion or passively by a secretionapparatus named secretion that consists of 12-16 proteins, and othersstay in periplasm fraction and are eventually degraded.

Some proteins may also be secreted by an autotransporter apparatus, suchas by utilizing an autotransporter domain. The proteins secreted byautotransporter domains typically comprise an N-terminal signal peptidethat plays a role in translocation to the periplasm, which may bemediated by secB or SRP pathways, passenger domain, and/or C-terminaltranslocation unit (UT) having a characteristic β-barrel structure. Theβ-barrel portion of the UT builds an aqueous pore channel across theouter membrane and helps the transportation of passenger domain tomedia. Autodisplayed passenger proteins are often cleaved by theautotransporter and set free to media.

The type I secretion machinery may also be used for the secretion ofrecombinant proteins in E. coli. The type I secretion machinery may beused for the secretion of high-molecular-weight toxins and exoenzymes.The type I secretion machinery consist of two inner membrane proteins(HlyB and HlyD) that are the member of the ATP binding cassette (ABC)transporter family, and an endogenous outer membrane protein (TolC). Thesecretion of recombinant proteins based on type I secretion machinerymay utilize the C-terminal region of α-haemolysin (HlyA) as a signalsequence. The recombinant proteins may readily pass through the innermembrane, periplasm, and outer membrane through the type I secretionmachinery.

Depending on the types of linker and signal peptides utilized by variousembodiments of the present application, both autotransporter and type Isecretion machinery can be altered to the cell surface displaymachinery. Alternatively, a system specific to cell surface display maybe used. For example, in this system, target proteins may be fused toPgsA protein (a poly-γ-glutamate synthetase complex) that is nativelydisplayed on the surface of Bacillus subtilis.

Certain embodiments may include lyases such as alginate lyases fusedwith various signal peptides and/or autotransporter domains found inproteins secreted by both type I and type II secretion machinery. Otherembodiments may include lyases such as alginate lyases fused with anycombination of signal peptides and or autotransporter domains found inproteins secreted transport machinery as described herein or known to aperson skilled in the art. Embodiments may also include signal peptidesor autotransporter domains that are experimentally redesigned tomaximize the secretion of lyases such as alginate lyases to the culturemedia, and may also include the use of many different linker sequencesthat fuse signal peptides, lyases, and autotransporters that improve theefficiency of secretion or the cell surface presentation of lyases.

Certain embodiments may include a microbial system or isolatedmicroorganism that comprise saccharide transporters, which are able totransport monosaccharides (e.g., DEHU) and oligosaccharides from themedia to the cytosol to efficiently utilize these monosaccharides as asource of carbon and/or energy. For instance, genes encodingmonosaccharide permeases (i.e., monosaccharide transporters) such asDEHU permeases may be isolated from bacteria that grow onpolysaccharides such as alginate as a source of carbon and/or energy,and may be incorporated into embodiments of the present microbial systemor isolated microorganism. As an additional example, embodiments mayalso include redesigned native permeases or transporters with alteredspecificity for monosaccharide (e.g., DEHU) transportation.

In this regard, E. coli contains several permeases able to transportmonosaccharides, which include, but are not limited to, KdgT for2-keto-3-deoxy-D-gluconate (KDG) transporter, ExuT for aldohexuronatessuch as D-galacturonate and D-glucuronate transporter, GntT, GntU, GntP,and GntT for gluconate transporter, and KgtP for proton-drivenα-ketoglutarate transporter. Microbial systems or recombinantmicroorganisms described herein may comprise any of these permeases, inaddition to those permeases known to a person of skill in the art andnot mentioned herein, and may also include permease enzymes redesignedto transport other monosaccharides, such as DEHU.

A microbial system or recombinant microorganism according to the presentinvention may also comprise permeases/transporters/superchannels/porinsthat catalyze the transport of monosaccharides (e.g., D-mannuronate andD-lyxose) from media to the periplasm or cytosol of a microorganism. Forexample, genes encoding the permeases of D-mannuronate in soil Aeromonasmay be incorporated into a microbial system as described herein.

As one alternative example, a microbial system or microorganism maycomprise native permeases/transporters that are redesigned to altertheir specificity for efficient monosaccharide transportation, such asfor D-mannuronate and D-lyxose transportation. For instance, E. colicontains several permeases that are able to transport monosaccharides orsugars such as D-mannonate and D-lyxose, including KdgT for2-keto-3-deoxy-D-gluconate (KDG) transporter, ExuT for aldohexuronatessuch as D-galacturonate and D-glucuronate transporter, GntPTU forgluconate/fructuronate transporter, uidB for glucuronide transporter,fucP for L-fucose transporter, galP for galactose transporter, yghK forglycolate transporter, dgoT for D-galactonate transporter, uhpT forhexose phosphate transporter, dctA for orotate/citrate transporter,gntUT for gluconate transporter, malEGF for maltose transporter: alsABCfor D-allose transporter, idnT for L-idonate/D-gluconate transporter,KgtP for proton-driven α-ketoglutarate transporter, lacY forlactose/galactose transporter, xylEFGH for D-xylose transporter, araEFGHfor L-arabinose transporter, and rbsABC for D-ribose transporter. Incertain embodiments, a microbial system or recombinant microorganism maycomprise permeases or transporters as described above, including thosethat are re-designed or optimized for improvided transport of certainmonosaccharides, such as D-mannuronate, DEHU, and D-lyxose.

Certain aspects may employ a recombinant microorganism that comprises a“superchannel,” by which aquatic or marine-biomass polysaccharides suchas alginate polymers, or fruit or vegetable biomass such as pectinpolymers, may be directly incorporated into the cytosol and degradedinside the microbial system. For instance, a group of bacteriacharacterized as Sphingomonads have a wide range in capability ofdegrading environmentally hazardous compounds such as polychlorinatedpolycyclic aromatics (dioxin). These bacteria contain characteristiclarge pleat-like molecules on their cell surfaces. In this regard,certain Sphingomonads have structures characterized as “superchannels”that enable the bacteria to directly take up macromolecules.

As one particular example of a microorganism comprising a superchannel,Sphingomonas sp. strain Al directly incorporates polysaccharides such asalginate through a superchannel. Such superchannels may consist of a piton the outer membrane (e.g., AlgR), alginate-binding proteins in theperiplasm (e.g., AlgQ1 and Alg Q2), and an ATP-binding cassette (ABC)transporter (e.g., AlgM1, AlgM2, and AlgS). Incorporated polysaccharidessuch as alginate may be readily depolymerized by lyases such as alginatelyases produced in the cytosol. Thus, certain embodiments mayincorporate genes encoding a superchannel (e.g., ccpA, algS, algM1,algM2, algQ1, algQ2) to introduce this ability to the microbial systemor recombinant microorganism. Other embodiments may includemicroorganisms such as Sphingomonas subarctica IFO 16058^(T), whichharbor the plasmid containing genes that encode a superchannel, andwhich have significantly improved ability to utilize marine or aquaticbiomass polysaccharides such as alginate as a source of carbon and/orenergy. Certain recombinant microorganisms may employ these superchannelencoding plasmid sequences contained within Sphingomonas subarctica IFO16058^(T).

Certain examples of alginate ABC transporters that may be utilizedherein, include ABC transporters Atu3021, Atu3022, Atu3023, Atu3024,algM1, algM2, AlgQ1, AlgQ2, AlgS, OG2516_(—)05558, OG2516_(—)05563,OG2516_(—)05568, and OG2516_(—)05573, including functional variantsthereof. Certain examples of alginate symporters that may be utilizedherein include symporters V12B01_(—)24239 and V12B01_(—)24194, amongothers, including functional variants thereof. One additional example ofan alginate porin includes V12B01_(—)24269, and variants thereof.

As noted above, certain embodiments may include recombinantmicroorganisms that comprise one or more monosaccharide dehydrogenases,isomerases, dehydratases, kinases, and aldolases. With regard tomonosaccharide dehydrogenases, certain microbial systems or recombinantmicroorganism may incorporate enzymes that reduce variousmonosaccharides (e.g., DEHU, mannuronate) to a monosaccharide that issuitable for biofuel biosynthesis, such as 2-keto-3-deoxy-D-gluconate(KDG) or D-mannitol. Such exemplary enzymes, include, for example, DEHUhydrogenases and mannuronate hydrogenases, in addition to variousalcohol dehydrogenases having DEHU hydrogenase and/or mannuronatedehydrogenase activity, such as the novel ADH1 through ADH12 enzymesisolated from Agrobacterium tumefaciens C58 (see, e.g., SEQ IDNOS:69-92).

For more detail on the ADH1 through ADH12 enzymes, SEQ ID NO:69 showsthe nucleotide and SEQ ID NO:70 shows the polypeptide sequence of ADH1Atu1557 isolated from Agrobacterium tumefaciens C58. SEQ ID NO:71 showsthe nucleotide and SEQ ID NO:72 shows the polypeptide sequence of ADH2Atu2022 isolated from Agrobacterium tumefaciens C58. SEQ ID NO:73 showsthe nucleotide and SEQ ID NO:74 shows the polypeptide sequence of ADH3Atu0626 isolated from Agrobacterium tumefaciens C58.

SEQ ID NO:75 shows the nucleotide and SEQ ID NO:76 shows the polypeptidesequence of ADH4 Atu5240 isolated from Agrobacterium tumefaciens C58.SEQ ID NO:77 shows the nucleotide and SEQ ID NO:78 shows the polypeptidesequence of ADH5 Atu3163 isolated from Agrobacterium tumefaciens C58.SEQ ID NO:79 shows the nucleotide and SEQ ID NO:80 shows the polypeptidesequence of ADH6 Atu2151 isolated from Agrobacterium tumefaciens C58.

SEQ ID NO:81 shows the nucleotide and SEQ ID NO:82 shows the polypeptidesequence of ADH7 Atu2814 isolated from Agrobacterium tumefaciens C58.SEQ ID NO:83 shows the nucleotide and SEQ ID NO:84 shows the polypeptidesequence of ADH8 Atu5447 isolated from Agrobacterium tumefaciens C58.SEQ ID NO:85 shows the nucleotide and SEQ ID NO:86 shows the polypeptidesequence of ADH9 Atu4087 isolated from Agrobacterium tumefaciens C58.

SEQ ID NO:87 shows the nucleotide and SEQ ID NO:88 shows the polypeptidesequence of ADH10 Atu4289 isolated from Agrobacterium tumefaciens C58.

SEQ ID NO:89 shows the nucleotide and SEQ ID NO:90 shows the polypeptidesequence of ADH11 Atu3027 isolated from Agrobacterium tumefaciens C58.SEQ ID NO:91 shows the nucleotide and SEQ ID NO:92 shows the polypeptidesequence of ADH12 Atu3026 isolated from Agrobacterium tumefaciens C58.

Further examples of enzymes having dehydrogenase activity includeAtu3026, Atu3027, OG2516_(—)05543, OG2516_(—)05538 and V12B01_(—)24244.The microorganisms and methods of the present invention may also utilizebiologically active fragments and variants of these hydrogenase enzymes,including optimized variants thereof.

As a further example, Pseudomonas grown using alginate as a sole sourceof carbon and energy comprises a DEHU hydrogenase enzyme that uses NADPHas a co-factor, is more stable when NADP⁺ is present in the solution,and is active at ambient pH. Thus, certain embodiments of a microbialsystem or a recombinant microorganism as described herein mayincorporate genes encoding hydrogenases such as DEHU or mannuronatehydrogenase derived or obtained from various microbes, in which thesemicrobes may be capable of growing on polysaccharides such as alginateor pectin as a source of carbon and/or energy.

Certain embodiments may incorporate components of a microbial system orisolated microorganism that is capable of efficiently growing onmonosaccharides such as D-mannuronate or D-lyxose as a source of carbonand energy. For instance, both Aeromonas and Aerobacter aerogenes PRL-R3comprise genes encoding monosaccharide dehydrogenases such asD-mannuronate hydrogenase and D-lyxose isomerase. Thus, certainmicrobial systems or recombinant microorganisms may comprisemonosaccharide dehydrogenases such as D-mannuronate hydrogenase andD-lyxose isomerase from Aeromonas, Aerobacter aerogenes PRL-R3, orvarious other suitable microorganisms, including those microorganismscapable of growing on D-mannuronate or D-lyxose as a source of carbonand energy.

Certain embodiments may include a microbial system or isolatedmicroorganism with enhanced efficiency for converting monosaccharidessuch as D-mannonate and D-xylulose into monosaccharides suitable for abiofuel biosynthesis pathway such as KDG. Merely by way of explanation,D-mannonate and D-xylulose are metabolites in microbes such as E. coli.D-mannonate is converted by a D-mannonate dehydratase to KDG. D-xyluloseenters the pentose phosphate pathway. Thus, to increase conversion ofD-mannonate to KDG, an exogenous or endogenous D-mannonate dehydratase(e.g., uxuA) gene may be over-expressed an a recombinant microorganismof the invention. Similarly, in other embodiments, suitable endogenousor exogenous genes such as kinases (e.g., kdgK), nad, as well as KDGaldolases (e.g., kdgA and eda) may be either incorporated oroverexpressed in a given recombinant microorganism (see SEQ IDNOS:93-96), including biologically active variants or fragments thereof,such as optimized variants of these genes. SEQ ID NO:93 shows thenucleotide sequence and SEQ ID NO:94 shows the polypeptide sequence of a2-keto-deoxy gluconate kinase (KdgK) from Escherichia coli DH10B. SEQ IDNO:95 shows the nucleotide sequence and SEQ ID NO:96 shows thepolypeptide sequence of a 2-keto-deoxy gluconate-6-phosphate aldorase(KdgA) from Escherichia coli DH10B.

In certain aspects, as noted above, a recombinant microorganism that iscapable of growing on alginate or pectin as a sole source of carbon mayutilize a naturally-occurring or endogenous copy of a dehyradratase,kinase, and/or aldolase. For instance, E. coli contains endogenousdehydratases, kinases, and aldolases that are capable of catalyzing theappropriate steps in the conversion of polysaccharides to a suitablemonosaccharide. In these and other related aspects, thenaturally-occurring dehydratase or kinase may also be over-expressed,such as by providing an exogenous copy of the naturally-occurringdehydratase, kinase or aldolase operable linked to a highly constitutiveor inducible promoter.

As one exemplary source of enzymes for engineering a recombinantmicroorganism to grow on alginate as a sole source of carbon, Vibriosplendidus is known to be able to metabolize alginate to support growth.For example, SEQ ID NO:1 shows a secretome region carrying certainVibrio splendidus genes (V12B01_(—)02425 to V12B01_(—)02480), whichencodes a type II secretion apparatus. SEQ ID NO:2 shows the nucleotidesequence of an entire genomic region between V12B01_(—)24189 toV12B01_(—)24249, which was derived from Vibrio splendidus, and whichwhen transformed into E. coli as a fosmid clone was sufficient to conferthe ability to grow on alginate as a sole source of carbon. SEQ IDNOS:3-64 show the individual putative genes contained within SEQ IDNO:2. Thus, in certain aspects, a recombinant microorganism (e.g., E.coli) that is able to grow on alginate as a sole source of carbon and/orenergy may comprise one or more nucleotide or polypeptide referencesequences described in SEQ ID NOS:1-64, including biologically activefragments or variants thereof, such as optimized variants.

In certain aspects, a recombinant microorganism that is able to grow onalginate as a sole source of carbon may contain certain codingnucleotide or polypeptide sequences contained within SEQ ID NO:2, suchas the sequences in SEQ ID NOS:3-64, or biologically active fragments orvariants thereof, including optimized variants. These sequences aredescribed in further detail below.

SEQ ID NO:3 shows the nucleotide coding sequence of the putative proteinV12B01_(—)24184. This putative coding sequence is contained within thepolynucleotide sequence of SEQ ID NO:2, and encodes a polypeptide thatis similar to an autotransporter adhesion or type I secretion targetggxgxdxxx (SEQ ID NO:145) repeat. SEQ ID NO:4 shows the polypeptidesequence of putative protein V12B01_(—)24184, encoded by thepolynucleotide of SEQ ID NO:3. This putative polypeptide is similar toautotransporter adhesion or type I secretion target ggxgxdxxx (SEQ IDNO:145) repeat.

SEQ ID NO:5 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24189. SEQ ID NO:6 shows the polypeptide sequence ofthe putative protein V12B01_(—)24189, which is similar tocyclohexadienyl dehydratase.

SEQ ID NO:7 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24194. SEQ ID NO:8 shows the polypeptide sequence ofthe putative protein V12B01_(—)24194, which is similar to a Na/prolinetransporter.

SEQ ID NO:9 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24199. SEQ ID NO:10 shows the polypeptide sequence ofthe putative protein V12B01_(—)24199, which is similar to aketo-deoxy-phosphogluconate aldolase.

SEQ ID NO:11 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24204. SEQ ID NO:12 shows the polypeptide sequence ofthe putative protein V12B01_(—)24204, which is similar to2-dehydro-3-deoxygluconokinase.

SEQ ID NO:13 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)241209. SEQ ID NO:14 shows the polypeptide sequence ofthe putative protein V12B01_(—)241209.

SEQ ID NO:15 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24214. SEQ ID NO:16 shows the polypeptide sequence ofthe putative protein V12B01_(—)24214, which is similar to a chondroitinAC/alginate lyase.

SEQ ID NO:17 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24219. SEQ ID NO:18 shows the polypeptide sequence ofthe putative protein V12B01_(—)24219, which is similar to a chondroitinAC/alginate lyase.

SEQ ID NO:19 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24224. SEQ ID NO:20 shows the polypeptide sequence ofthe putative protein V12B01_(—)24224, which is similar to a2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase.

SEQ ID NO:21 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24229. SEQ ID NO:22 shows the polypeptide sequence ofthe putative protein V12B01_(—)24229, which is similar to a GntR-familytranscriptional regulator.

SEQ ID NO:23 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24234. SEQ ID NO:24 shows the polypeptide sequence ofthe putative protein V12B01_(—)24234, which is similar to a Na⁺/prolinesymporter.

SEQ ID NO:25 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24239. SEQ ID NO:26 shows the polypeptide sequence ofthe putative protein V12B01_(—)24239, which is similar to anoligoalginate lyase.

SEQ ID NO:27 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24244. SEQ ID NO:28 shows the polypeptide sequence ofputative protein V12B01_(—)24244, which is similar to a3-hydroxyisobutyrate dehydrogenase.

SEQ ID NO:29 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24249. SEQ ID NO:30 shows the polypeptide sequence ofthe putative protein V12B01_(—)24249, which is similar to amethyl-accepting chemotaxis protein.

SEQ ID NO:31 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24254. SEQ ID NO:32 shows the polypeptide sequence ofputative protein V12B01_(—)24254, which is similar to an alginate lyase.

SEQ ID NO:33 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24259. SEQ ID NO:34 shows the polypeptide sequence ofputative protein V12B01_(—)24259, which is similar to an alginate lyase.

SEQ ID NO:35 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24264. SEQ ID NO:36 shows the polypeptide sequence ofputative protein V12B01_(—)24264.

SEQ ID NO:37 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24269. SEQ ID NO:38 shows the polypeptide sequence ofputative protein V12B01_(—)24269, which is similar to a putativeoligogalacturonate specific porin.

SEQ ID NO:39 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)24274. SEQ ID NO:40 shows the polypeptide sequence ofputative protein V12B01_(—)24274, which is similar to an alginate lyase.

FIG. 32 shows the nucleotide coding sequence and polypeptide sequence ofputative protein V12B01_(—)02425. FIG. 32A shows the nucleotide sequencethat encodes the putative protein V12B01_(—)02425 (SEQ ID NO:41). FIG.32B shows the polypeptide sequence of putative protein V12B01_(—)02425(SEQ ID NO:42), which is similar to a type II secretory pathwaycomponent EpsC.

SEQ ID NO:43 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02430. SEQ ID NO:44 shows the polypeptide sequence ofputative protein V12B01_(—)02430, which is similar to a type IIsecretory pathway component EpsD.

SEQ ID NO:45 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02435. SEQ ID NO:46 shows the polypeptide sequence ofputative protein V12B01_(—)02435, which is similar to a type IIsecretory pathway component EpsE.

SEQ ID NO:47 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02440. SEQ ID NO:48 shows the polypeptide sequence ofputative protein V12B01_(—)02440, which is similar to a type IIsecretory pathway component EpsF.

SEQ ID NO:49 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02445. SEQ ID NO:50 shows the polypeptide sequence ofputative protein V12B01_(—)02445, which is similar to a type IIsecretory pathway component EpsG.

SEQ ID NO:51 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02450. SEQ ID NO:52 shows the polypeptide sequence ofputative protein V12B01_(—)02450, which is similar to a type IIsecretory pathway component EpsH.

SEQ ID NO:53 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02455. SEQ ID NO:54 shows the polypeptide sequence ofputative protein V12B01_(—)02455, which is similar to a type IIsecretory pathway component EpsI.

SEQ ID NO:55 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02460. SEQ ID NO:56 shows the polypeptide sequence ofputative protein V12B01_(—)02460, which is similar to a type IIsecretory pathway component EpsJ.

SEQ ID NO:57 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02465. SEQ ID NO:58 shows the polypeptide sequence ofputative protein V12B01_(—)02465, which is similar to a type IIsecretory pathway component EpsK.

SEQ ID NO:59 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02470. SEQ ID NO:60 shows the polypeptide sequence ofputative protein V12B01_(—)02470, which is similar to a type IIsecretory pathway component EpsL.

SEQ ID NO:61 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02475. SEQ ID NO:62 shows the polypeptide sequence ofputative protein V12B01_(—)02475, which is similar to a type IIsecretory pathway component EpsM.

SEQ ID NO:63 shows the nucleotide sequence that encodes the putativeprotein V12B01_(—)02480. SEQ ID NO:64 shows the nucleotide sequence thatencodes the putative protein V12B01_(—)02480, which is similar to a typeII secretory pathway component EpsC.

As a further exemplary source of enzymes for engineering a microorganismto grow on alginate, Agrobacterium tumefaciens C58 is able to metabolizerelatively small sizes of alginate molecules (1000 mers) as a solesource of carbon and energy. Since A. tumefaciens C58 has long been usedfor plant biotechnology, the genetics of this organism has beenrelatively well studied, and many genetic tools are available andcompatible with other gram-negative bacteria such as E. coli. Thus,certain aspects may employ this microbe, or the genes therein, for theproduction of suitable monosaccharides. For instance, as noted above,the present disclosure provides a series of novel ADH genes having bothDEHU and mannuronate hydrogenase activity that were obtained fromAgrobacterium tumefaciens C58 (see SEQ ID NOS: 67-92).

As noted above, certain aspects may include a recombinant microorganismor microbial system that is capable of growing on pectin as a solesource of carbon and/or energy. Pectin is a linear chain ofα-(1-4)-linked D-galacturonic acid that forms the pectin-backbone, ahomogalacturonan. Into this backbone, there are regions wheregalacturonic acid is replaced by (1-2)-linked L-rhamnose. From rhamnose,side chains of various neutral sugars typically branch off. This type ofpectin is called rhamnogalacturonan I. Over all, about up to every 25thgalacturonic acid in the main chain is exchanged with rhamnose. Somestretches consisting of alternating galacturonic acid andrhamnose—“hairy regions”, others with lower density of rhamnose—“smoothregions.” The neutral sugars mainly comprise D-galactose, L-arabinoseand D-xylose; the types and proportions of neutral sugars vary with theorigin of pectin. In nature, around 80% of carboxyl groups ofgalacturonic acid are esterified with methanol. Some plants, likesugar-beet, potatoes and pears, contain pectins with acetylatedgalacturonic acid in addition to methyl esters. Acetylation preventsgel-formation but increases the stabilising and emulsifying effects ofpectin. Certain pectin degradation and metabolic pathways areexemplified in FIG. 3.

In addition to the genes, enzymes, and biological pathways describedabove, certain recombinant microorganisms may incorporate features thatare useful for growth on pectin as a sole source of carbon. Forinstance, to degrade and metabolize pectin as a sole source of carbon,pectin methyl and acetyl esterases first catalyze the hydrolysis ofmethyl and acetyl esters on pectin. Examples of pectin methyl esterasesinclude, but are not limited to, pemA and pmeB. Examples of pectinacetyl esterases include, but are not limited to, PaeX and PaeY. Furtherexamples of pectin methyl esterases that may be utilized herein includeenzymes or polypeptides sharing at least 60%, 70%, 80%, 90%, 95%, 98%,or more sequence identity (including all integers in between) to thepectate methyl esterases in FIG. 40. Further examples of pectate acetylesterases that may be utilized herein include enzymes or polypeptidessharing at least 60%, 70%, 80%, 90%, 95%, 98%, or more sequence identity(including all integers in between) to the pectate acetyl esterasesdescribed in FIG. 41.

Further to this end, pectate lyases and hydrolases may catalyze theendolytic cleavage of pectate via β-elimination and hydrolysis,respectively, to produce oligopectates. Other enzymes that may beutilized to metabolize pectin include Examples of pectate lyasesinclude, but are not limited to, PelA, PelB, PelC, PelD, PelE, Pelf,PelI, PelL, and PelZ. Examples of pectate hydrolases include, but arenot limited to, PehA, PehN, PehV, PehW, and PehX. Further examples ofpectate lyases include polypeptides or enzymes sharing at least 60%,70%, 80%, 90%, 95%, 98%, or more sequence identity (including allintegers in between) to the pectate lyases described in FIG. 38.

Polygalacturonases, rhamnogalacturonan lyases, and rhamnogalacturonanhydrolyases may also be utilized herein to degrade and metabolizepectin. Examples of rhamnogalacturonan lyases include polypeptides orenzymes sharing at least 60%, 70%, 80%, 90%, 95%, 98%, or more sequenceidentity (including all integers in between) to the rhamnoglacturonanlyases (i.e., rhamnogalacturonases) described in FIG. 39A. Examples ofrhamnogalacturonate hydrolyases include polypeptides or enzymes sharingat least 60%, 70%, 80%, 90%, 95%, 98%, or more sequence identity(including all integers in between) to the rhamnogalacturonatehydrolases described in FIG. 39B.

Thus, to degrade and metabolize pectin, certain of the recombinantmicroorganisms and methods of the present invention may incorporate oneor more of the above noted methy and acetyl esterases, lyases, and/orhydrolases, among others known in the art. These may enzymes may beencoded and expressed by endogenous or exogenous genes, and may alsoinclude biologically active fragments or variants thereof, such ashomologs, orthologs, and/or optimized variants of these enzymes.

To further metabolize the degradation products of pectin, oligopectatesmay be transported into the periplasm fraction of gram-negative bacteriaby outer membrane porins, where they are further degraded into suchcomponents as di- and tri-galactonurates. Examples of outer membraneporins include that can transport oligopectates into the periplasminclude, but are not limited to, kdgN and kdgM. Certain recombinantmicroorganism may incorporate these or similar genes.

Di- and tri-galactonurates may then be transported into the cytosol forfurther degradation. Bacteria contain at least two different transportersystems responsible for di- and tri-galacturonate transportation,including symporter and ABC transporter (e.g., TogT and TogMNAB,respectively). Thus, certain of the recombinant microorganisms providedherein may comprise one or more a di- or tri-galacturonate transoportersystems, such as TogT and/or TogMNAB.

Once di- and trigalacturonate are incorporated into the cytosol, shortpectate or galacturonate lyases, break them down to D-galacturonate and(4S)-4,6-dihydroxy-2,5-dioxohexuronate. Examples of short pectate orgalacturonate lyases include, but are not limited to, PelW and Ogl,which genes may be either endogenously or exogenously incorporated intocertain recombinant microorganisms provided herein. D-galacturonate and(4S)-4,6-dihydroxy-2,5-dioxohexuronate are then converted to5-dehydro-4-deoxy-D-glucuronate and further to KDG, which steps may becatalyzed by KduI and KduD, respectively. The KduI enzyme has anisomerase activity, and the KduD enzyme has a dehydrogenase activity,such as a 2-deoxy-D-gluconate 3-dehydrogenase activity. Accordingly,certain recombinant microorgansms provided herein may comprise one ormore short pectate or galacturonate lyases, such as PelW and/or Ogl, andmay optionally comprise one or more isomerases, such as KduI, as well asone or more dehydrogenases, such as KduD, to convert di- andtrigalacturonates into a suitable monosaccharide, such as KDG.

In certain aspects, a recombinant microorganism, such as E. coli, thatis able to grown on pectin or tri-galacturonate as a sole source ofcarbon and/or energy may comprise one or more of the gene sequencescontained within SEQ ID NOS:65 and 66, including biologically activefragments or variants thereof, such as optimized variants. SEQ ID NO:65shows the nucleotide sequence of the kdgF-PaeX region from Erwiniacarotovora subsp. Atroseptica SCRI1043. SEQ ID NO:66 shows thenucleotide sequence of ogl-kdgR from Erwinia carotovora subsp.Atroseptica SCRI1043.

In certain aspects, a recombinant microorganism, such as E. coli, thatis able to grown on pectin or tri-galacturonate as a sole source ofcarbon and/or energy may comprise one or more genomic regions of Erwiniachrysanthemi, comprising several genes (kdgF, kduI, kduD, pelW, togM,togN, togA, togB, kdgM, paeX, ogl, and kdgR) encoding enzymes (kduI,kduD, ogl, pelW, and paeX), transporters (togM, togN, togA, togB, andkdgM), and regulatory proteins (kdgR) responsible for degradation of di-and trigalacturonate, as well as several genes (pelA, pelE, paeY, andpem) encoding pectate lyases (pelA and pelE), pectin acetylesterases(paeY), and pectin methylesterase (pem) (see Example 2).

Additional examples of isomerases that may be utilized herein includeglucoronate isomerases, such as those in the family uxaC, as well as4-deoxy-L-threo-5-hexylose uronate isomerases, such as those in thefamily KduI. Additional examples of reductases that may be utilizedherein include tagaturonate reductases, such as those in the familyuxaB. Additional examples of dehyadratases that may be utilized hereininclude altronate dehydratases, such as those in the family uxaA.Additional examples of dehydrogenases that may be utilized hereininclude 2-deoxy-D-gluconate 3-dehydrogenases, such as those in thefamily kduD.

Certain aspects my also utilize recombinant microorganisms engineered toenhance the efficiency of the KDG degradation pathway. For instance, inbacteria, KDG is a common metabolic intermediate in the degradation ofhexuronates such as D-glucuronate and D-galacturonate and enters intoEntner Doudoroff pathway where it is converted to pyruvate andglyceraldehyde-3-phosphate (G3P). In this pathway, KDG is firstphosphorylated by KDG kinase (KdgK) followed by its cleavage intopyruvate and glyceraldehyde-3-phosphate (G3P) using2-keto-3-deoxy-D-6-posphate-gluconate (KDPG) aldolase (KdgA). Theexpression of these enzymes concurrently with KDG permease (e.g., KdgT)is negatively regulated by KdgR and is almost none at basal level. Theexpression is dramatically (3-5-fold) induced upon the addition ofhexuronates, and a similar result has been reported in Pseudomonas grownon alginate. Hence, to increase the conversion of KDG to pyruvate andG3P, the negative regulator KdgR may be removed. To further improve thepathway efficiency, exogenous copies of KdgK and KdgA may also beincorporated into a given recombinant microorganism.

In certain aspects, a recombinant microorganism that is able to grow ona polysaccharide (e.g., alginate, pectin, etc) as a sole source ofcarbon may be capable of producing an increased amount of a givencommodity chemical (e.g., ethanol) while growing on that polysaccharide.For example, E. coli engineered to grown on alginate may be engineeredto produced an increased amount of ethanol from alginate as compared toE. coli that is not engineered to grown on alginate (see Example 11).Thus, certain aspects include a recombinant microorganism that iscapable of growing on alginate or pectin as a sole source carbon, andthat is capable of producing an increased amount of ethanol, such as bycomprising one or more genes encoding and expressing a pyruvatedecarboxylase (pdc) and/or an alcohol dehydrogenase, includingfunctional variants thereof. In certain aspects, such a recombinantmicroorganism may comprise a pyruvate decarboxylase (pdc) and twoalcohol dehydrogenases (adhA and adhB) obtained from Zymomonas mobilis.

Embodiments of the present invention also include methods for convertingpolysaccharide to a suitable monosaccharide comprising, (a) obtaining apolysaccharide; (b) contacting the polysaccharide with a chemicalcatalysis or enzymatic pathway, thereby converting the polysaccharide toa first monosaccharide or oligosaccharide; and (c) contacting the firstmonosaccharide with a microbial system for a time sufficient to convertthe first monosaccharide or oligosaccharide to the suitablemonosaccharide, wherein the microbial system comprises, (i) at least onegene encoding and expressing an enzyme selected from a monosaccharidetransporter, a disaccharide transporter, a trisaccharide transporter, anoligosaccharide transporter, and a polysaccharide transporter; and (ii)at least one gene encoding and expressing an enzyme selected from amonosaccharide dehydrogenase, an isomerase, a dehydratase, a kinase, andan aldolase, thereby converting the polysaccharide to a suitablemonosaccharide.

In certain aspects of the present invention, aquatic or marine-biomasspolysaccharides such as alginate may be chemically degraded usingchemical catalysts such as acids. Similarly, biomass-derived pectin maybe chemically degraded. For instance, the reaction catalyzed by chemicalcatalysts is typically through hydrolysis, as opposed to theβ-elimination type of reactions catalyzed by enzymatic catalysts. Thus,certain embodiments may include boiling alginate or pectin with strongmineral acids to liberate carbon dioxide from D-mannuronate, therebyforming D-lyxose, a common sugar metabolite utilized by manymicroorganisms. Such embodiments may use, for example, formate,hydrochloric acid, sulfuric acid, in addition to other suitable acidsknown in the art as chemical catalysts.

An enzymatic pathway may utilized one or more enzymes described hereinthat are capable of catalyzing the degradation of polysaccharides, suchas alginate or pectin.

Other embodiments may use variations of chemical catalysis similar tothose described herein or known to a person skilled in the art,including improved or redesigned methods of chemical catalysis suitablefor use with biomass related polysaccharides. Certain embodimentsinclude those wherein the resulting monosaccharide uronate isD-mannuronate.

As noted above, the suitable monosaccharides or suitableoligosaccharides produced by the recombinant microorganisms andmicrobial systems of the present invention may be utilized as afeedstock in the production of commodity chemicals, such as biofuels, aswell as commodity chemical intermediates. Thus, certain embodiments ofthe present invention relate generally to methods for converting asuitable monosaccharide or oligosaccharide to a commodity chemical, suchas a biofuel, comprising, (a) obtaining a suitable monosaccharide oroligosaccharide; (b) contacting the suitable monosaccharide oroligosaccharide with a microbial system for a time sufficient to convertto the suitable monosaccharide to the biofuel, thereby converting thesuitable monosaccharide to the biofuel.

Certain aspects include methods for converting a suitable monosaccharideto a first commodity chemical such as a biofuel, comprising, (a)obtaining a suitable monosaccharide; (b) contacting the suitablemonosaccharide with a microbial system for a time sufficient to convertto the suitable monosaccharide to the first commodity chemical, whereinthe microbial system comprises one or more genes encoding a aldehyde orketone biosynthesis pathway, thereby converting the suitablemonosaccharide to the first commodity chemical.

In these and other related aspects, depending on the particular ketoneor aldehyde biosynthesis pathway employed, the first commodity chemicalmay be further enzymatically and/or chemically reduced and dehydrated toa second commodity chemical. Examples of such second commodity chemicalsinclude, but are not limited to, butene or butane; 1-phenylbutene or1-phenylbutane; pentene or pentane; 2-methylpentene or 2-methylpentane;1-phenylpentene or 1-phenylpentane; 1-phenyl-4-methylpentene or1-phenyl-4-methylpentane; hexene or hexane; 2-methylhexene or2-methylhexane; 3-methylhexene or 3-methylhexane; 2,5-dimethylhexene or2,5-dimethylhexane; 1-phenylhexene or 1-phenylhexane;1-phenyl-4-methylhexene or 1-phenyl-4-methylhexane;1-phenyl-5-methylhexene or 1-phenyl-5-methylhexane; heptene or heptane;2-methylheptene or 2-methylheptane; 3-methylheptene or 3-methylheptane;2,6-dimethylheptene or 2,6-dimethylheptane; 3,6-dimethylheptene or3,6-dimethylheptane; 3-methyloctene or 3-methyloctane; 2-methyloctene or2-methyloctane; 2,6-dimethyloctene or 2,6-dimethyloctane;2,7-dimethyloctene or 2,7-dimethyloctane; 3,6-dimethyloctene or3,6-dimethyloctane; and cyclopentane or cyclopentene.

Certain embodiments of the present invention may also include methodsfor converting a suitable monosaccharide or oligosaccharide to acommodity chemical comprising (a) obtaining a suitable monosaccharide oroligosaccharide; (b) contacting the suitable monosaccharide oroligosaccharide with a microbial system for a time sufficient to convertto the suitable monosaccharide or oligosaccharide to the commoditychemical, wherein the microbial system comprises; (i) one or more genesencoding a biosynthesis pathway; (ii) one or more genes encoding andexpressing a C—C ligation pathway; and (iii) one or more genes encodingand expressing a reduction and dehydration pathway, comprising a dioldehydrogenase, a diol dehydratase, and a secondary alcoholdehydrogenase, thereby converting the suitable monosaccharide oroligosaccharide to the commodity chemical.

Certain aspects also include recombinant microorganism that comprise (i)one or more genes encoding a biosynthesis pathway; (ii) one or moregenes encoding and expressing a C—C ligation pathway; and (iii) one ormore genes encoding and expressing a reduction and dehydration pathway,comprising a diol dehydrogenase, a diol dehydratase, and a secondaryalcohol dehydrogenase. Certain aspects also include recombinantmicroorganisms that comprise the above pathways individually or incertain combinations, such as recombinant microorganism that comprisesone or more genes encoding a biosynthesis pathway, as described herein.Certain aspects may also include recombinant microorganisms thatcomprise one or more genes encoding and expressing a C—C ligationpathway, as described herein. Certain aspects may also includerecombinant microorganisms that comprise one or more genes encoding andexpressing a reduction and dehydration pathway, comprising a dioldehydrogenase, a diol dehydratase, and a secondary alcoholdehydrogenase, as described herein.

As for recombinant microorganisms that comprise combinations of theabove-noted pathways, certain aspects may include recombinantmicroorganisms that comprise (i) one or more genes encoding abiosynthesis pathway; and (ii) one or more genes encoding and expressinga C—C ligation pathway. Certain aspects may also include recombinantmicroorganisms that comprise (i) one or more genes encoding andexpressing a C—C ligation pathway; and (ii) one or more genes encodingand expressing a reduction and dehydration pathway, comprising a dioldehydrogenase, a diol dehydratase, and a secondary alcoholdehydrogenase.

Certain aspects may also include recombinant microorganisms thatcomprise one or more individual components of a dehydration andreduction pathway, such as a recombinant microorganism that comprises adiol dehydrogenase, a diol dehydratase, or a secondary alcoholdehydrogenase. These and other microorganisms may be utilized, forexample, to convert a suitable polysaccharide to a first commoditychemical, or an intermediate thereof, or to convert a first commoditychemical, or an intermediate thereof, to a second commodity chemical.

Merely by way of illustration, a recombinant microorganism comprising aC—C ligation pathway may be utilized to convert butanal into a firstcommodity chemical, or an intermediate thereof, such as5-hydroxy-4-octanone, which can then be converted into a secondcommodity chemical, or intermediate thereof, by any suitable pathway. Asa further example, a recombinant microorganism comprising a C—C ligationpathway and a diol hydrogenase may be utilized for the sequentialconversion of butanal into 5-hydroxy-4-octanone and then4,5-octanonediol. Examples of recombinant microorganisms that comprisethese and other various combinations of the individual pathwaysdescribed herein, as well as various combinations of the individualcomponents of those pathways, will be apparent to those skilled in theart, and may also be found in the Examples.

Also included are methods of converting a polysaccharide to a firstcommodity chemical, or an intermediate thereof, such as by utilizing arecombinant microorganism that comprises an aldehyde or ketonebiosynthesis pathway. Also included are methods of converting a firstcommodity chemical, or intermediate thereof, to a second commoditychemical, such as by utilizing a recombinant microorganism thatoptionally comprises a biosynthesis pathway, optionally comprises C—Cligation pathway and/or optionally comprises one or more of theindividual components of a dehydration and reduction pathway. Merely byway of illustration, a recombinant microorganism comprising an exogenousC—C ligase (e.g., benzaldehyde lyase from Pseudomonas fluorescens) couldbe utilized in a method to convert a first commodity chemical such as3-methylbutanal to a second commodity chemical such as2,7-dimethyl-5-hydroxy-4-octanone. Along this line of illustration, thesame or different recombinant microorganism comprising a dioldehydrogenase could be utilized in a method to convert2,7-dimethyl-5-hydroxy-4-octanone to another commodity chemical such as2,7-dimethyl-4,5-octanediol (see Table 2 for other examples). As anadditional illustrative example, a recombinant microorganism comprisingan exogenous secondary alcohol dehydrogenase could be utilized in amethod to convert a first commodity chemical such as2,7-dimethyl-4-octanone to a second commodity chemical such as2,7-dimethyloctanol.

Embodiments of a microbial system or isolated microorganism of thepresent application may include a naturally-occurring biosynthesispathway, and/or an engineered, reconstructed, or re-designedbiosynthesis pathway that has been optimized for improved functionality.

Embodiments of a microbial system or recombinant microorganism of thepresent invention may include a natural or reconstructed biosynthesispathway, such as a butyraldehyde biosynthesis pathway, as found in suchmicroorganisms as Clostridium acetobutylicum and Streptomycescoelicolor. In explanation, butyrate and butanol are the commonfermentation products of certain bacterial species such as Clostridia,in which the production of butyrate and butanol is mediated by asynthetic thiolase dependent pathway characteristically similar to fattyacid degradation pathway. Such pathways may be initiated with thecondensation of two molecules of acetyl-CoA to acetoacetyl-CoA, which iscatalyzed by thiolase. Acetoacetyl-CoA is then reduced to β-hydroxybutyryl-CoA, which is catalyzed by NAD(P)H dependent β-hydroxybutyryl-CoA dehydrogenase (HBDH). Crotonase catalyzes dehydration fromβ-hydroxy butyryl-CoA to form crotonyl-CoA. Further reduction catalyzedby NADH-dependent butyryl-CoA dehydrogenase (BCDH) saturates the doublebond at C2 of crotonyl-CoA to form butyryl-CoA.

In certain embodiments, thiolase, the first enzyme in this pathway, maybe overexpressed to maximize production. In certain embodiments,thiolase may over-expressed in E. coli. In this regard, all threeenzymes (e.g., HBDH, crotonase, and BCDH) catalyzing the followingreaction steps are found in Clostridium acetobutylicum ATCC824. Incertain embodiments, BDH, crotonase, and BCDH may be expressed orover-expressed in a suitable microorganism such as E. coli.Alternatively, a short-chain aliphatic acyl-CoA dehydrogenase derivedfrom Pseudomonas putida KT2440 may be utilized in other embodiments of amicrobial system or isolated microorganism of the present application.

Further to this end, butyryl-CoA in Clostridia may be readily convertedto butanol and/or butyrate by at least a few different pathways. In onepathway, butyryl-CoA is directly reduced to butyraldehyde catalyzed byNADH dependent CoA-acylating aldehyde dehydrogenase (ALDH).Butyraldehyde may be further reduced to butanol by NADH-dependentbutanol dehydrogenase. Although CoA-acylating ALDH catalyzes the onestep reduction of butyryl-CoA to butyraldehyde, the incorporation ofCoA-acylating ALDH to the microbial system may result in acetoaldehydeformation because of its promiscuous acetyl-CoA deacylating activity. Incertain embodiments, the formation of acetoaldehyde may be minimized byfunctionally redesigning the relevant enzyme(s).

Butyryl-CoA in other biosynthesis pathways is deacylated to form butyrylphosphate catalyzed by phosphotransbutyrylase. Butyryl phosphate is thenhydrolyzed by reversible butyryl phosphate kinase to form butyrate. Thisreaction is coupled with ATP generation from ADP. The butyrate formationthrough these enzymes is known to be significantly more specific.Certain embodiments may comprise phosphotransbutyrylase and butyrylphosphate kinase to the microbial system. In other embodiments, butyratemay be directly formed from butyryl-CoA by short chain acyl-CoAthioesterase.

Butyrate in Clostridia may also be sequentially reduced to butanol,which is catalyzed by a single alcohol/aldehyde dehydrogenase. Certainembodiments may comprise short chain aldehyde dehydrogenase from otherbacteria such as Pseudomonas putida to complement the production ofbutyraldehyde in the microbial system. One potential concern in usingshort chain aldehyde dehydrogenase involves the possible formation ofacetoaldehyde from acetate. Certain embodiments may be directed tominimizing the acetate formation in the microbial system, for example,by deleting several genes encoding enzymes involved in the acetateproduction.

Moreover, there are multiple routes in E. coli to form acetate, one ofwhich is mediated by pyruvate oxygenase (POXB) from pyruvate, whereasanother is mediated by phosphotransacetylase (PTA) and acetyl phosphatekinase (ACKA) from acetyl-CoA. The acetate production from E. colimutant strains with poxB⁻, pta⁻, and acka⁻ are significantly diminished.In addition, incorporation of acetyl-CoA synthase (ACS) which catalysesthe acetyl-CoA formation from acetate is also known to significantlyreduce the accumulation of acetate. Certain embodiments may comprise amicrobial system or isolated microorganism with deleted POXB, PTA,and/or ACKA genes, and other embodiments may also comprise, separatelyor together with the deleted genes, one or more genes encoding andexpressing ACS.

A microbial system or recombinant microorganism provided herein may alsocomprise a glutaraldehyde biosynthesis pathway. As one example,Saccharomyces cerevisiae has a lysine biosynthetic pathway in whichacetyl-CoA is initially condensed to α-ketoglutarate, a commonmetabolite in citric acid cycle, to form homocitorate. This reaction iscatalyzed by homocitrate synthase derived from Yeast, Thermusthermophilus, or Deinococcus radiodurans. Homoaconitase derived fromYeast, Thermus thermophilus, or Deinococcus radiodurans catalyzes theconversion between homocitrate and homoisocitrate. Homoisocitrate isthen oxidatively decarboxylated to form 2-ketoadipate, which iscatalyzed by homoisocitrate dehydrogenase derived from Yeast, Thermusthermophilus, or Deinococcus radiodurans. Homoisocitrate is alsooxidatively decarboxylated to form glutaryl-CoA, which may be catalyzedby homoisocitrate dehydrogenase. Thus, certain embodiments may comprisea homocitrate synthase, a homoaconitase, and/or a homoisocitratedehydrogenase.

Further to this end, in synthesizing 2-keto-adipicsemialdehyde,2-ketoadipate is reduced to 2-keto-adipicsemialdehyde. This reaction canbe catalyzed by dialdehyde dehydrogenase, which, for example, may beisolated from Agrobacterium tumefaciens C58. Thus, certain embodimentsmay incorporate dialdehyde dehydrogenases into a microbial system orrecombinant microorganism.

In synthesizing glutaraldehyde, Acyl-CoA thioesterases (ACOT) may alsocatalyze the hydrolysis of glutaryl-CoA. The genes encoding(β-carboxylic acyl-CoA specific peroxisomal ACOTs are found in manymammalian species; both ACOT4 and ACOT8 derived from mice have beenpreviously expressed in E. coli and shown that both enzymes are highlyactive on the hydrolysis of glutaryl-CoA to form glutarate. Certainembodiments may comprise one or more Acyl-CoA thioesterases.

Glutarate is sequentially reduced to glutaraldehyde. This reaction canbe catalyzed by glutaraldehyde dehydrogenase (CpnE), which, for example,may be isolated from Comomonas sp. Strain NCIMB 9872. Certainembodiments may incorporate glutaraldehyde dehydrogenases such as CpnEinto a microbial system or isolated microorganism. Other embodiments maycomprise both ACOT and CpnE enzymes. Other embodiments may comprise CpnEenzymes redesigned to catalyze the reduction of 1-hydroxy propanoate andsuccinate to 1-hydroxy propanal and succinicaldehyde.

In certain aspects, the biosynthesis pathway may include an aldehydebiosynthesis pathway, a ketone biosynthesis pathway, or both. In certainaspects, the biosynthesis pathway may be include one or more of anacetoaldehyde, propionaldehyde, butyraldehyde, isobutyraldehyde,2-methyl-butyraldehyde, 3-methyl-butyraldehyde, 4-methylpentaldehyde,phenylacetoaldehyde, 2-phenyl acetoaldehyde,2-(4-hydroxyphenyl)acetaldehyde, 2-Indole-3-acetoaldehyde,glutaraldehyde, 5-amino-pentaldehyde, succinate semialdehyde, and/orsuccinate 4-hydroxyphenyl acetaldehyde biosynthesis pathway, includingvarious combinations thereof.

With regard to combinations of biosynthesis pathways, a biosynthesispathway may comprise an acetoaldehyde biosynthesis pathway incombination with at least one of a propionaldehyde, butyraldehyde,isobutyraldehyde, 2-methyl-butyraldehyde, 3-methyl-butyraldehyde, orphenylacetoaldehyde biosynthesis pathway. In certain aspects, abiosynthesis pathway may comprise a propionaldehyde biosynthesis pathwayin combination with at least one of a butyraldehyde, isobutyraldehyde,2-methyl-butyraldehyde, 3-methyl-butyraldehyde, or phenylacetoaldehydebiosynthesis pathway. In certain aspects, a biosynthesis pathway maycomprise a butyraldehyde biosynthesis pathway in combination with atleast one of an isobutyraldehyde, 2-methyl-butyraldehyde,3-methyl-butyraldehyde, or phenylacetoaldehyde biosynthesis pathway. Incertain aspects, a biosynthesis pathway may comprise an isobutyraldehydebiosynthesis pathway in combination with at least one of a2-methyl-butyraldehyde, 3-methyl-butyraldehyde, or phenylacetoaldehydebiosynthesis pathway. In certain aspects, a biosynthesis pathway maycomprise a 2-methyl-butyraldehyde biosynthesis pathway in combinationwith at least one of a 3-methyl-butyraldehyde or a phenylacetoaldehydebiosynthesis pathway. In certain aspects, a biosynthesis pathway maycomprise a 3-methyl-butyraldehyde biosynthesis pathway in combinationwith a phenylacetoaldehyde biosynthesis pathway.

In certain aspects, a propionaldehyde biosynthesis pathway may comprisea threonine deaminase (ilvA) gene from an organism such as Escherichiacoli and a keto-isovalerate decarboxylase (kivd) gene from an organismsuch as Lactococcus lactis, and/or functional variants of these enzymes,including homologs or orthologs thereof, as well as optimized variants.These enzymes may be utilized generally to convert L-threonine topropionaldehyde.

In certain aspects, a butyraldehyde biosyntheis pathway may comprise atleast one of a thiolase (atoB) gene from an organism such as E. coli, aβ-hydroxy butyryl-CoA dehydrogenase (hbd) gene, a crotonase (crt) gene,a butyryl-CoA dehydrogenase (bcd) gene, an electron transferflavoprotein A (etfA) gene, and/or an electron transfer flavoprotein B(etfB) gene from an organism such as Clostridium acetobutyricum (e.g.,ATCC 824), as well as a coenzyme A-linked butyraldehyde dehydrogenase(ald) gene from an organism such as Clostridium beijerinckiiacetobutyricum ATCC 824. In certain aspects, a coenzyme A-linked alcoholdehydrogenase (adhE2) gene from an organism such as Clostridiumacetobutyricum ATCC 824 may be used as an alternative to an ald gene.

In certain aspects, an isobutyraldehyde biosynthetic pathway maycomprise an acetolactate synthase (alsS) from an organism such asBacillus subtilis or an als gene from an organism such as Klebsiellapneumoniae subsp. pneumoniae MGH 78578 (codon usage may be optimized forE. coli protein expression). Such a pathway may also compriseacetolactate reductoisomerase (ilvC) and/or 2,3-dihydroxyisovaleratedehydratase (ilvD) genes from an organism such as E. coli, as well as aketo-isovalerate decarboxylase (kivd) gene from an organism such asLactococcus lactis.

In certain aspects, a 3-methylbutyraldehyde and 2-methylbutyraldehydebiosynthesis pathway may comprise an acetolactate synthase (alsS) genefrom an organism such as Bacillus subtilis or an (als) gene from anorganism such as Klebsiella pneumoniae subsp. pneumoniae MGH 78578(codon usage may be optimized for E. coli protein expression). Certainaspects of such a pathway may also comprise acetolactatereductoisomerase (ilvC), 2,3-dihydroxyisovalerate dehydratase (ilvD),isopropylmalate synthase (LeuA), isopropylmalate isomerase (LeuC andLeuD), and 3-isopropylmalate dehydrogenase (LeuB) genes from an organismsuch as E. coli, as well as a keto-isovalerate decarboxylase (kivd) froman organism such as Lactococcus lactis.

In certain aspects, a phenylacetoaldehyde and4-hydroxyphenylacetoaldehyde biosynthesis pathway may comprise one ormore of 3-deoxy-7-phosphoheptulonate synthase (aroF, aroG, and aroH),3-dehydroquinate synthase (aroB), a 3-dehydroquinate dehydratase (aroD),dehydroshikimate reductase (aroE), shikimate kinase II (aroL), shikimatekinase I (aroK), 5-enolpyruvylshikimate-3-phosphate synthetase (aroA),chorismate synthase (aroC), fused chorismate mutase P/prephenatedehydratase (pheA), and/or fused chorismate mutase T/prephenatedehydrogenase (tyrA) genes from an organism such as E. coli, as well asa keto-isovalerate decarboxylase (kivd) from an organism such asLactococcus lactis.

In certain aspects, such as for the ultimate production of1,10-diamino-5-decanol and 1,10-dicarboxylic-5-decanol, a biosynthesispathway may comprise one or more homocitrate synthase, homoaconitatehydratase, homoisocitrate dehydrogenase, and/or homoisocitratedehydrogenase genes from an organism such as Deinococcus radioduransand/or Thermus thermophilus, as well as a keto-adipate decarboxylasegene, a 2-aminoadipate transaminase gene, and aL-2-Aminoadipate-6-semialdehyde: NAD+6-oxidoreductase gene. Such abiosynthesis pathway would be able to convert α-ketoglutarate to5-aminopentaldehyde.

In certain aspects, such as for one step in cyclopentanol production, aα-ketoadipate semialdehyde biosynthesis pathway may comprise homocitratesynthase (hcs), homoaconitate hydratase, and homoisocitratedehydrogenase genes from an organism such as Deinococcus radioduransand/or Thermus thermophilus, and an α-ketoadipate semialdehydedehydrogenase gene. Such a biosynthesis pathway would be able to convertacetyl-CoA and α-ketoglutarate to α-ketoadipate semialdehyde.

For the production of certain commodity chemicals, such as2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and indole-3-ethanol, amongother similar chemicals, a biosynthesis pathway (e.g., aldehydebiosynthesis pathway) may optionally or further comprise one or moregenes encoding a carboxylase enzyme, such as an indole-3-pyruvatedecarboxylase (IPDC). An IPDC may be obtained, for example, from suchmicroorganisms as Azospirillum brasilense and Paenibacillus polymyxaE681. In this regard, an IPDC may be utilized to more efficientlycatalyze the dexarboxylation of various carboxylic acids to form thecorresponding aldehyde, which can be further converted to a commoditychemical by a reductase or dehydrogenase, as detailed herein.

In certain aspects, a 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and2-(indole-3-)ethanol biosynthesis pathway may comprise a transketolase(tktA), a 3-deoxy-7-phosphoheptulonate synthase (aroF, aroG, and aroH),3-dehydroquinate synthase (aroB), a 3-dehydroquinate dehydratase (aroD),a dehydroshikimate reductase (aroE), a shikimate kinase II (aroL), ashikimate kinase I (aroK), a 5-enolpyruvylshikimate-3-phosphatesynthetase (aroA), a chorismate synthase (aroC, a fused chorismatemutase P/prephenate dehydratase (pheA), and a fused chorismate mutaseT/prephenate dehydrogenase (tyrA) genes from E. coli, keto-isovaleratedecarboxylase (kivd) from Lactococcus lactis, alcohol dehydrogenase(adh2) from Saccharomyces cerevisiae, Indole-3-pyruvate decarboxylase(ipdc) from Azospirillum brasilense, phenylethanol reductase (par) fromRhodococcus sp. ST-10, and abenzaldehyde lyase (bal) from Pseudomonasfluorescence.

As for all other pathways described herein, the components for each ofthe biosynthesis pathways described herein may be present in arecombinant microorganism either endogenously or exogenously. To improvethe efficiency of a given biosynthesis pathway, endogenous genes, forexample, may be up-regulated or over-expressed, such as by introducingan additional (i.e., exogenous) copy of that endogenous gene into therecombinant microorganism. Such pathways may also be optimized byaltering via mutagenesis the endogenous version of a gene to improvefunctionality, followed by introduction of the altered gene into themicroorganism. The expression of endogenous genes may be up ordown-regulated, or even eliminated, according to known techniques in theart and described herein. Similarly, the expression levels ofexogenously provided genes may be regulated as desired, such as by usingvarious constitutive or inducible promoters. Such genes may also be“codon-optimized,” as described herein and known in the art. Alsoincluded are functional naturally-occurring variants of the genes andenzymes described herein, including homologs or orthologs thereof.

Certain embodiments of a microbial system or isolated microorganism maycomprise a CC-ligation pathway. In certain aspects, a CC-ligationpathway may comprise a ThDP-dependent enzyme, such as a C—C ligase, oran optimized C—C ligase. For example, eight-carbon unit molecules(butyroins) may be made from condensing together two four-carbon unitmolecules (butyraldehydes). ThDP-dependent enzymes are a group ofenzymes known to catalyze both breaking and formation of C—C bonds andhave been utilized as catalysts in chemoenzymatic syntheses. Thespectrum of chemical reactions that these enzymes catalyze ranges fromdecarboxylation of α-keto acids, oxidative decarboxylation,carboligation, and to the cleavage of C—C bonds.

To provide a few examples, benzaldehyde lyase (BAL) from Pseudomonasfluorescens, benzoylformate decarboxylase (BFD) from Pseudomonas putida,and pyruvate decarboxylase (PDC) from Zymomonas mobilis may catalyze acarboligation reaction between two aldehydes. BAL accepts the broadestspectrum of aldehydes as substrates among these three enzymes rangingfrom substituted benzaldehyde to acetoaldehyde, among others, as shownherein. BAL catalyzes stereospecific carboligation reaction between twoaldehydes and forms α-hydroxy ketone swith over 99% ee forR-configuration. The benzoin formation from two benzaldehyde moleculesis a favored reaction catalyzed by BAL and proceeds as fast as 320 μmol(benzoin) mg (protein)⁻¹ min⁻¹. The formation of α-hydroxy ketone may becarried out using many different aldehydes, including butyraldehyde.

BFD and PCD may also catalyze the carboligation reactions between twoaldehyde molecules. BFD and PCD accept relatively larger and smalleraldehyde molecules, respectively. With the presence of benzaldehyde andacetoaldehyde, BFD catalyzes the formation of benzoin and (S)-α-hydroxyphenylpropanone (2S-HPP), whereas PCD catalyzes the formation of(R)-α-hydroxy phenylpropanone (2R-HPP) and (R)-α-hydroxy 2-butanone(acetoin). As detailed below, certain microbial systems or isolatedmicroorganisms of the present application may comprise natural oroptimized C—C ligases (ThDP-dependent enzymes) selected frombenzaldehyde lyase (BAL) from Pseudomonas fluorescens benzoylformatedecarboxylase (BFD) from Pseudomonas putida, and pyruvate decarboxylase(PDC) from Zymomonas mobilis. Other embodiments may comprise abenzaldehyde lyase (BAL) from Pseudomonas fluorescens (see SEQ IDNOS:143-144, showing the nucleotide and polypeptide sequences,respectively) including biologically active variants thereof, such asoptimized variants.

A C—C ligation pathway of the present invention typically comprises oneor more C—C ligases, such as a lyase enzyme. Exemplary lyases include,but are not limited to, acetoaldehyde lyases, propionaldehyde lyases,butyraldehyde lyases, isobutyraldehyde lyases, 2-methyl-butyraldehydelyases, 3-methyl-butyraldehyde lyases (isoveraldehyde),phenylacetaldehyde lyases, α-keto adipate carboxylyases, pentaldehydelyases, 4-methyl-pentaldehyde lyases, hexyldehyde lyases, heptaldehydelyases, octaldehyde lyases, 4-hydroxyphenylacetaldehyde lyases,indoleacetaldehyde lyases, indolephenylacetaldehyde lyases. In certainaspects, a selected CC-ligase or lyase enzyme may have one or more ofthe above exemplified lyase activities, such as acetoaldehyde lyaseactivity, a propionaldehyde lyase activity, a butyraldehyde lyaseactivity, and/or an isobutyraldehyde lyase activity, among others.

As noted above, a C—C ligase may comprise a benzaldehyde lyase, such asa benzaldehyde lyase isolated from Pseudomonas fluorescens (SEQ IDNOS:143-144), as well as biologically active fragments or variants ofthis reference sequence, such as optimized variants of a benzaldehydelyase. In this regard, certain aspects may comprise nucleotide sequencesor polypeptide sequences having 80%, 85%, 90%, 95%, 97%, 98%, 99%sequence identity to SEQ ID NOS:143-144, and which are capable ofcatalyzing a carboligation reaction, or which possess C—C lyaseactivity, as described herein. In certain aspects, a BAL enzyme willcomprise one or more conserved amino acid residues, including G27, E50,A57, G155, P162, P234, D271, G277, G422, G447, D448, and/or G512.

Pseudomonas fluorescens is able to grow on R-benzoin as the sole carbonand energy source because it harbours the enzyme benzaldehyde lyase thatcleaves the acyloin linkage using thiamine diphosphate (ThDP) as acofactor. In the reverse reaction, as utilized herein, benzaldehydelyase catalyses the carboligation of two aldehydes with high substrateand stereospecificity. Structure-based comparisons with other proteinsshow that benzaldehyde lyase belongs to a group of closely relatedThDP-dependent enzymes. The ThDP cofactors of these enzymes are fixed attheir two ends in separate domains, suspending a comparatively mobilethiazolium ring between them. While the residues binding the two ends ofThDP are well conserved, the lining of the active centre pocket aroundthe thiazolium moiety varies greatly within the group. The active sitesfor BAL have been described, for example, in Kneen et al (Biochimica etBiophysica Acta 1753:263-271, 2005) and Brandt et al. (Biochemistry47:7734-43, 2008). Benzaldehyde lyase derived from Pseudomonasfluorescens has been demonstrated herein to at least have anacetoaldehyde lyase activity, a propionaldehyde lyase activity, abutyraldehyde lyase activity, a 3-methyl-butyraldehyde lyase activity, apentaldehyde lyase activity, a 4-methylpentaldehyde lyase activity, ahexyldehyde lyase activity, a phenylacetoaldehyde lyase activity, and anoctaldehyde lyase activity (see Table 2), among other in vivo lyaseactivities (see FIGS. 48-55).

In certain aspects, a C—C ligase, such as BAL derived from Pseudomonasfluorescens, BFD derived from Pseudomonas putida, or PDC derived fromZymomonas mobilis may comprise a lyase with a combination of lyaseactivities, such as a lyase having both a propionaldehyde lyase activityand a 3-methyl-butyraldehyde lyase activity, among other combinationsand activities, such as those exemplary combinations detailed herein.Merely by way of illustration, a lyase having a combination of lyaseactivities may be referred to herein as apropionaldehyde/3-methyl-butyraldehyde lyase.

A dehydration and reduction pathway, comprising a diol dehydrogenase, adiol dehydratase, and a secondary alcohol dehydrogenase, may be utilizedto further convert an aldehyde, ketone, or corresponding alcohol, to acommodity chemical, such as a biofuel.

To this end, a dehydration and reduction pathway may comprise one ormore diol dehydrogenases. A “diol dehydrogenase” refers generally to anenzyme that catalyzes the reversible reduction and oxidation of aα-hydroxy ketone and/or its corresponding diol. Certain embodiments of amicrobial system or isolated microorganism may comprise genes encoding adiol dehydrogenase that specifically catalyzes the reduction ofα-hydroxy-ketones, including, for example, a 4, 5, octanedioldehydrogenase. Diol dehydrogenases, such as 4, 5, octanedioldehydrogenase, may be isolated from a variety of organisms andincorporated into a microbial system or isolated microorganism. Aparticular group of alcohol dehydrogenases has a characteristic abilityto oxidize various α-hydroxy alcohols and reduce various α-hydroxyketones and α-keto ketones. As such, the recitation “diol dehydrogenase”may also encompass such alcohol dehydrogenases.

By way of example regarding diol dehydrogenases from exemplaryorganisms, glycerol dehydrogenase isolated from Hansenula ofunaensis hasbroad substrate specificity and is capable of catalyzing the oxidationof various α-hydroxy alcohols, including 1,2-octane, as well as thereduction of various α-hydroxy ketones and α-keto ketones, including3-hydroxy-2-butanone and 3,4-hexanedione, with the activity comparableto its native substrates, glycerol and dihydroxyaceton, respectively(40-200%). As one further example, glycerol dehydrogenase discovered inHansenula polumorpha DI-1 works similarly. In certain embodiments, amicrobial system or recombinant microorganism may comprise a glyceroldehydrogenase gene isolated from Hansenula ofunaensis, a glyceroldehydrogenase isolated from Hansenula polumorpha DI-1 and/or ameso-2,3-butane diol dehydrogenase from Klebsiella pneumoniae. In otherembodiments, a microbial system or isolated microorganism may comprise a4, 5, octanediol dehydrogenase, among others detailed herein. Dioldehyodregnases may also be obtained from Lactobaccilus brevis ATCC 367,Pseudomanas putida KT2440, and Klebsiella pneumoniae MGH78578), asdescribed herein (see Example 5).

Exemplary diol dehydrogenases include, but are not limited to,2,3-butanediol dehydrogenase, 3,4-hexanediol dehydrogenase,4,5-octanediol dehydrogenase, 5,6-decanediol dehydrogenase,6,7-dodecanediol dehydrogenase, 7,8-tetradecanediol dehydrogenase,8,9-hexadecanediol dehydrogenase, 2,5-dimethyl-3,4-hexanedioldehydrogenase, 3,6-dimethyl-4,5-octanediol dehydrogenase,2,7-dimethyl-4,5-octanediol dehydrogenase, 2,9-dimethyl-5,6-decanedioldehydrogenase, 1,4-diphenyl-2,3-butanediol dehydrogenase,bis-1,4-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase,1,4-diindole-2,3-butanediol dehydrogenase, 1,2-cyclopentanedioldehydrogenase, 2,3-pentanediol dehydrogenase, 2,3-hexanedioldehydrogenase, 2,3-heptanediol dehydrogenase, 2,3-octanedioldehydrogenase, 2,3-nonanediol dehydrogenase, 4-methyl-2,3-pentanedioldehydrogenase, 4-methyl-2,3-hexanediol dehydrogenase,5-methyl-2,3-hexanediol dehydrogenase, 6-methyl-2,3-heptanedioldehydrogenase, 1-phenyl-2,3-butanediol dehydrogenase,1-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase,1-indole-2,3-butanediol dehydrogenase, 3,4-heptanediol dehydrogenase,3,4-octanediol dehydrogenase, 3,4-nonanediol dehydrogenase,3,4-decanediol dehydrogenase, 3,4-undecanediol dehydrogenase,2-methyl-3,4-hexanediol dehydrogenase, 5-methyl-3,4-heptanedioldehydrogenase, 6-methyl-3,4-heptanediol dehydrogenase,7-methyl-3,4-octanediol dehydrogenase, 1-phenyl-2,3-pentanedioldehydrogenase, 1-(4-hydroxyphenyl)-2,3-pentanediol dehydrogenase,1-indole-2,3-pentanediol dehydrogenase, 4,5-nonanediol dehydrogenase,4,5-decanediol dehydrogenase, 4,5-undecanediol dehydrogenase,4,5-dodecanediol dehydrogenase, 2-methyl-3,4-heptanediol dehydrogenase,3-methyl-4,5-octanediol dehydrogenase, 2-methyl-4,5-octanedioldehydrogenase, 8-methyl-4,5-nonanediol dehydrogenase,1-phenyl-2,3-hexanediol dehydrogenase,1-(4-hydroxyphenyl)-2,3-hexanediol dehydrogenase,1-indole-2,3-hexanediol dehydrogenase, 5,6-undecanediol dehydrogenase,5,6-undecanediol dehydrogenase, 5,6-tridecanediol dehydrogenase,2-methyl-3,4-octanediol dehydrogenase, 3-methyl-4,5-nonanedioldehydrogenase, 2-methyl-4,5-nonanediol dehydrogenase,2-methyl-5,6-decanediol dehydrogenase, 1-phenyl-2,3-heptanedioldehydrogenase, 1-(4-hydroxyphenyl)-2,3-heptanediol dehydrogenase,1-indole-2,3-heptanediol dehydrogenase, 6,7-tridecanediol dehydrogenase,6,7-tetradecanediol dehydrogenase, 2-methyl-3,4-nonanedioldehydrogenase, 3-methyl-4,5-decanediol dehydrogenase,2-methyl-4,5-decanediol dehydrogenase, 2-methyl-5,6-undecanedioldehydrogenase, 1-phenyl-2,3-octanediol dehydrogenase,1-(4-hydroxyphenyl)-2,3-octanediol dehydrogenase,1-indole-2,3-octanediol dehydrogenase, 7,8-pentadecanedioldehydrogenase, 2-methyl-3,4-decanediol dehydrogenase,3-methyl-4,5-undecanediol dehydrogenase, 2-methyl-4,5-undecanedioldehydrogenase, 2-methyl-5,6-dodecanediol dehydrogenase,1-phenyl-2,3-nonanediol dehydrogenase,1-(4-hydroxyphenyl)-2,3-nonanediol dehydrogenase,1-indole-2,3-nonanediol dehydrogenase, 2-methyl-3,4-undecanedioldehydrogenase, 3-methyl-4,5-dodecanediol dehydrogenase,2-methyl-4,5-dodecanediol dehydrogenase, 2-methyl-5,6-tridecanedioldehydrogenase, 1-phenyl-2,3-decanediol dehydrogenase,1-(4-hydroxyphenyl)-2,3-decanediol dehydrogenase,1-indole-2,3-decanediol dehydrogenase, 2,5-dimethyl-3,4-heptanedioldehydrogenase, 2,6-dimethyl-3,4-heptanediol dehydrogenase,2,7-dimethyl-3,4-octanediol dehydrogenase,1-phenyl-4-methyl-2,3-pentanediol dehydrogenase,1-(4-hydroxyphenyl)-4-methyl-2,3-pentanediol dehydrogenase,1-indole-4-methyl-2,3-pentanediol dehydrogenase,2,6-dimethyl-4,5-octanediol dehydrogenase, 3,8-dimethyl-4,5-nonanedioldehydrogenase, 1-phenyl-4-methyl-2,3-hexanediol dehydrogenase,1-(4-hydroxyphenyl)-4-methyl-2,3-hexanediol dehydrogenase,1-indole-4-methyl-2,3-hexanediol dehydrogenase,2,8-dimethyl-4,5-nonanediol dehydrogenase,1-phenyl-5-methyl-2,3-hexanediol dehydrogenase,1-(4-hydroxyphenyl)-5-methyl-2,3-hexanediol dehydrogenase,1-indole-5-methyl-2,3-hexanediol dehydrogenase,1-phenyl-6-methyl-2,3-heptanediol dehydrogenase,1-(4-hydroxyphenyl)-6-methyl-2,3-heptanediol dehydrogenase,1-indole-6-methyl-2,3-heptanediol dehydrogenase,1-(4-hydroxyphenyl)-4-phenyl-2,3-butanediol dehydrogenase,1-indole-4-phenyl-2,3-butanediol dehydrogenase,1-indole-4-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase,1,10-diamino-5,6-decanediol dehydrogenase,1,4-di(4-hydroxyphenyl)-2,3-butanediol, 2,3-hexanediol-1,6-dicarboxylicacid dehydrogenase, and the like.

In certain aspects, a selected diol dehydrogenase enzyme may have one ormore of the above exemplified diol dehydrogenase activities, such as a2,3-butanediol dehydrogenase activity, a 3,4-hexanediol dehydrogenaseactivity, and/or a 4,5-octanediol dehydrogenase activity, among others.

In certain aspects, a recombinant microorganism may comprise a dioldehydrogenase encoded by a nucleotide reference sequence selected fromSEQ ID NO:97, 99, and 101, or an enzyme having a polyeptide sequenceselected from SEQ ID NO:98, 100, and 102, including biologically activefragments or variants thereof, such as optimized variants. Certainaspects may also comprises nucleotide sequences or polypeptide sequenceshaving 80%, 85%, 90%, 95%, 97%, 98%, 99% sequence identity to SEQ IDNOS:97-102.

Other embodiments may comprise re-designed diol dehydrogenases forreduction of 1-hydroxy propanal, succinicaldehyde, and glutaraldehyde to1,3-propanediol, 1,4-butanediol, and 1,5 pentanediol, respectively,among others.

A dehydration and reduction pathway, as described herein, may compriseone or more diol dehydratases. A “diol dehydratase” refers generally toan enzyme that catalyzes the irreversible dehydration of diols. Forinstance, this enzyme may serve to dehydrate octanediol to form4-octane. It has been recognized that there are at least two differenttypes of diol dehydratases: a group dependent on and independent ofcoenzyme B12 for its catalysis. Coenzyme B12 dependent diol dehydratasesare known to catalyze a radical mediated dehydration reaction fromα-hydroxy alcohol to aldehydes or ketones. For example, a dioldehydratase from Klebsiella pneumoniae catalyzes the dehydration ofglycerol to form β-hydroxypropyl aldehyde, accepts 2,3-butanediol as asubstrate, and catalyzes the dehydration reaction to form 2-butanone.

As a further example, Clostridium butylicum contains coenzyme B12independent diol dehydratases. FIG. 46 shows the in vivo biologicalactivity of coenzyme B12 independent diol dehydratase (dhaB1) andactivator (dhaB2) isolated from Clostridium butylicum (see Example 9).46A shows the in vivo production of 1-propanol from 1,2-propanediol,FIG. 46B shows the in vivo production of 2-butanol from meso-2,3butanediol, and FIG. 46C shows the in vivo production of cyclopentanonefrom trans-1,2-cyclopentanediol.

Thus, certain embodiments of the present invention may compriseoptimized or redesigned diol dehydratases that accommodate varioussubstrates, such as 4,5-octanediol as a substrate, and may include dioldehydratases isolated and/or optimized from Klebsiella pneumoniae andClostridium butylicum, among other organisms described herein and knownin the art.

Exemplary diol dehydratases include, but are not limited to,2,3-butanediol dehydratase, 3,4-hexanediol dehydratase, 4,5-octanedioldehydratase, 5,6-decanediol dehydratase, 6,7-dodecanediol dehydratase,7,8-tetradecanediol dehydratase, 8,9-hexadecanediol dehydratase,2,5-dimethyl-3,4-hexanediol dehydratase, 3,6-dimethyl-4,5-octanedioldehydratase, 2,7-dimethyl-4,5-octanediol dehydratase,2,9-dimethyl-5,6-decanediol dehydratase, 1,4-diphenyl-2,3-butanedioldehydratase, bis-1,4-(4-hydroxyphenyl)-2,3-butanediol dehydratase,1,4-diindole-2,3-butanediol dehydratase, 1,2-cyclopentanedioldehydratase, 2,3-pentanediol dehydratase, 2,3-hexanediol dehydratase,2,3-heptanediol dehydratase, 2,3-octanediol dehydratase, 2,3-nonanedioldehydratase, 4-methyl-2,3-pentanediol dehydratase,4-methyl-2,3-hexanediol dehydratase, 5-methyl-2,3-hexanedioldehydratase, 6-methyl-2,3-heptanediol dehydratase,1-phenyl-2,3-butanediol dehydratase, 1-(4-hydroxyphenyl)-2,3-butanedioldehydratase, 1-indole-2,3-butanediol dehydratase, 3,4-heptanedioldehydratase, 3,4-octanediol dehydratase, 3,4-nonanediol dehydratase,3,4-decanediol dehydratase, 3,4-undecanediol dehydratase,2-methyl-3,4-hexanediol dehydratase, 5-methyl-3,4-heptanedioldehydratase, 6-methyl-3,4-heptanediol dehydratase,7-methyl-3,4-octanediol dehydratase, 1-phenyl-2,3-pentanedioldehydratase, 1-(4-hydroxyphenyl)-2,3-pentanediol dehydratase,1-indole-2,3-pentanediol dehydratase, 4,5-nonanediol dehydratase,4,5-decanediol dehydratase, 4,5-undecanediol dehydratase,4,5-dodecanediol dehydratase, 2-methyl-3,4-heptanediol dehydratase,3-methyl-4,5-octanediol dehydratase, 2-methyl-4,5-octanedioldehydratase, 8-methyl-4,5-nonanediol dehydratase,1-phenyl-2,3-hexanediol dehydratase, 1-(4-hydroxyphenyl)-2,3-hexanedioldehydratase, 1-indole-2,3-hexanediol dehydratase, 5,6-undecanedioldehydratase, 5,6-undecanediol dehydratase, 5,6-tridecanedioldehydratase, 2-methyl-3,4-octanediol dehydratase,3-methyl-4,5-nonanediol dehydratase, 2-methyl-4,5-nonanedioldehydratase, 2-methyl-5,6-decanediol dehydratase,1-phenyl-2,3-heptanediol dehydratase,1-(4-hydroxyphenyl)-2,3-heptanediol dehydratase,1-indole-2,3-heptanediol dehydratase, 6,7-tridecanediol dehydratase,6,7-tetradecanediol dehydratase, 2-methyl-3,4-nonanediol dehydratase,3-methyl-4,5-decanediol dehydratase, 2-methyl-4,5-decanedioldehydratase, 2-methyl-5,6-undecanediol dehydratase,1-phenyl-2,3-octanediol dehydratase, 1-(4-hydroxyphenyl)-2,3-octanedioldehydratase, 1-indole-2,3-octanediol dehydratase, 7,8-pentadecanedioldehydratase, 2-methyl-3,4-decanediol dehydratase,3-methyl-4,5-undecanediol dehydratase, 2-methyl-4,5-undecanedioldehydratase, 2-methyl-5,6-dodecanediol dehydratase,1-phenyl-2,3-nonanediol dehydratase, 1-(4-hydroxyphenyl)-2,3-nonanedioldehydratase, 1-indole-2,3-nonanediol dehydratase,2-methyl-3,4-undecanediol dehydratase, 3-methyl-4,5-dodecanedioldehydratase, 2-methyl-4,5-dodecanediol dehydratase,2-methyl-5,6-tridecanediol dehydratase, 1-phenyl-2,3-decanedioldehydratase, 1-(4-hydroxyphenyl)-2,3-decanediol dehydratase,1-indole-2,3-decanediol dehydratase, 2,5-dimethyl-3,4-heptanedioldehydratase, 2,6-dimethyl-3,4-heptanediol dehydratase,2,7-dimethyl-3,4-octanediol dehydratase,1-phenyl-4-methyl-2,3-pentanediol dehydratase,1-(4-hydroxyphenyl)-4-methyl-2,3-pentanediol dehydratase,1-indole-4-methyl-2,3-pentanediol dehydratase,2,6-dimethyl-4,5-octanediol dehydratase, 3,8-dimethyl-4,5-nonanedioldehydratase, 1-phenyl-4-methyl-2,3-hexanediol dehydratase,1-(4-hydroxyphenyl)-4-methyl-2,3-hexanediol dehydratase,1-indole-4-methyl-2,3-hexanediol dehydratase,2,8-dimethyl-4,5-nonanediol dehydratase,1-phenyl-5-methyl-2,3-hexanediol dehydratase,1-(4-hydroxyphenyl)-5-methyl-2,3-hexanediol dehydratase,1-indole-5-methyl-2,3-hexanediol dehydratase,1-phenyl-6-methyl-2,3-heptanediol dehydratase,1-(4-hydroxyphenyl)-6-methyl-2,3-heptanediol dehydratase,1-indole-6-methyl-2,3-heptanediol dehydratase,1-(4-hydroxyphenyl)-4-phenyl-2,3-butanediol dehydratase,1-indole-4-phenyl-2,3-butanediol dehydratase,1-indole-4-(4-hydroxyphenyl)-2,3-butanediol dehydratase,1,10-diamino-5,6-decanediol dehydratase,1,4-di(4-hydroxyphenyl)-2,3-butanediol, 2,3-hexanediol-1,6-dicarboxylicacid dehydratase, and the like.

In certain aspects, a selected diol dehydratase enzyme may have one ormore of the above exemplified diol dehydratase activities, such as a2,3-butanediol dehydratase activity, a 3,4-hexanediol dehydrataseactivity, and/or a 4,5-octanediol dehydratase activity, among others.

In certain aspects, diol dehydratases may be obtained from Klebsiellapneumoniae MGH 78578, including from the pduCDE gene of this and othermicroorganisms. In certain aspects, a recombinant microorganism maycomprise one or more diol dehydratases encoded by a nucleotide referencesequence selected from SEQ ID NO:103, 105, and 107, or an enzyme havinga polyeptide sequence selected from SEQ ID NO:104, 106, and 108,including biologically active fragments or variants thereof, such asoptimized variants. Certain aspects may also comprises nucleotidesequences or polypeptide sequences having 80%, 85%, 90%, 95%, 97%, 98%,99% sequence identity to SEQ ID NOS:103-108. In certain aspects,polypeptides of SEQ ID NO:104 may comprise certain conserved amino acidresidues, including those chosen from D149, P151, A155, A159, G165,E168, E170, A183, G189, G196, Q200, E208, G215, Y219, E221, T222, S224,Y226, G227, T228, F232, G235, D236, D237, T238, P239, S241, L245, Y249,S251, R252, G253, K255, R257, S260, E265, M268, G269, S275, Y278, L279,E280, C283, G291, Q293, G294, Q296, N297, G298, G312, E329, S341, R344,G356, D371, N372, F374, S377, R392, D393, R412, L477, A486, G499, D500,S516, N522, D523, Y524, G526, and G530.

In certain aspects, a diol dehydratase may include a polypeptide thatcomprises an amino acid sequence having 0%, 85%, 90%, 95%, 97%, 98%, 99%sequence identity to SEQ ID NOS:308-311. SEQ ID NO:308 shows thepolypeptide sequence of PduG, a diol dehydratase reactivation largesubunit derived from Klebsiella pneumoniae subsp. pneumoniae MGH 78578.SEQ ID NO:309 shows the polypeptide sequence of PduH, diol dehydratasereactivation small subunit derived from Klebsiella pneumoniae subsp.pneumoniae MGH 78578. SEQ ID NO:310 shows the polypeptide sequence of aB12-independent glycerol dehydratase from Clostridium Butyricum. SEQ IDNO:311 shows the polypeptide sequence of a glycerol dehydrataseactivator from Clostridium Butyricum. In certain aspects, aB12-independent glycerol dehydratase may comprise conserved amino acidresidues, such as T36, G74, P87, E88, E97, W126, R221, A263, Q265, R287,D289, E309, R317, G335, G345, G346, N356, P374, R379, G399, G401, P403,D408, G432, C433, N452, C529, G533, G539, G540, S559, G603, N₆₀₄, A654,G658, R659, D676, N₇₀₂, Q735, N737, A747, P751, R760, V761, A762, G763,Q776, I780, and/or R782. In certain aspects, a B12-independent glyceroldehydratase activator may comprise certain conserved amino acidresidues, including D19, G20, G22, R24, F28, G31, C32, C36, W38, C39,N41, P42, C58, C64, C96, G129, T132, G135, G136, D185, R187, N₂₀₈, R222,and/or R264.

A dehydration and reduction pathway, as described herein, may compriseone or more alcohol dehydrogenases or secondary alcohol dehydrogenases.An “alcohol dehydrogenase” or “secondary alcohol dehydrogenase” that ispart of a dehydration and reduction pathway refers generally to anenzyme that catalyzes the conversion of aldehyde or ketone substituentsto alcohols. For instance, 4-octanone may be reduced to 4-octanol by asecondary alcohol dehydrogenase one enzymatic step for the conversion ofbutyroin to a biofuel. Pseudomonads express at least one secondaryalcohol dehydrogenase that oxidizes 4-octanol to 4-octanone using NAD+as a co-factor. As another example, Rhodococcus erythropolis ATCC4277catalyzes oxidation of medium to long chain secondary fatty alcoholsusing NADH as a co-factor, using an enzyme that also catalyzes theoxidation of 3-decanol and 4-decanol. In addition, Norcadia fuscaAKU2123 contains an (S)-specific secondary alcohol dehydrogenase.

Genes encoding secondary alcohol dehydrogenases may be isolated fromthese and other organisms according to known techniques in the art andincorporated into the microbial systems recombinant organisms asdescribed herein. In certain embodiments, a microbial system or isolatedmicroorganism may comprise natural or optimized secondary alcoholdehydrogenases from Pseudomonads, Rhodococcus erythropolis ATCC4277,Norcadia fusca AKU2123, or other suitable organisms.

Examples of secondary alcohol dehydrogenases include, but are notlimited to, 2-butanol dehydrogenase, 3-hexanol dehydrogenase, 4-octanoldehydrogenase, 5-decanol dehydrogenase, 6-dodecanol dehydrogenase,7-tetradecanol dehydrogenase, 8-hexadecanol dehydrogenase,2,5-dimethyl-3-hexanol dehydrogenase, 3,6-dimethyl-4-octanoldehydrogenase, 2,7-dimethyl-4-octanol dehydrogenase,2,9-dimethyl-4-decanol dehydrogenase, 1,4-diphenyl-2-butanoldehydrogenase, bis-1,4-(4-hydroxyphenyl)-2-butanol dehydrogenase,1,4-diindole-2-butanol dehydrogenase, cyclopentanol dehydrogenase, 2(or3)-pentanol dehydrogenase, 2(or 3)-hexanol dehydrogenase, 2(or3)-heptanol dehydrogenase, 2(or 3)-octanol dehydrogenase, 2(or3)-nonanol dehydrogenase, 4-methyl-2(or 3)-pentanol dehydrogenase,4-methyl-2(or 3)-hexanol dehydrogenase, 5-methyl-2(or 3)-hexanoldehydrogenase, 6-methyl-2(or 3)-heptanol dehydrogenase, 1-phenyl-2(or3)-butanol dehydrogenase, 1-(4-hydroxyphenyl)-2(or 3)-butanoldehydrogenase, 1-indole-2(or 3)-butanol dehydrogenase, 3(or 4)-heptanoldehydrogenase, 3(or 4)-octanol dehydrogenase, 3(or 4)-nonanoldehydrogenase, 3(or 4)-decanol dehydrogenase, 3(or 4)-undecanoldehydrogenase, 2-methyl-3(or 4)-hexanol dehydrogenase, 5-methyl-3 (or4)-heptanol dehydrogenase, 6-methyl-3 (or 4)-heptanol dehydrogenase,7-methyl-3(or 4)-octanol dehydrogenase, 1-phenyl-2(or 3)-pentanoldehydrogenase, 1-(4-hydroxyphenyl)-2(or 3)-pentanol dehydrogenase,1-indole-2(or 3)-pentanol dehydrogenase, 4(or 5)-nonanol dehydrogenase,4(or 5)-decanol dehydrogenase, 4(or 5)-undecanol dehydrogenase, 4(or5)-dodecanol dehydrogenase, 2-methyl-3(or 4)-heptanol dehydrogenase,3-methyl-4(or 5)-octanol dehydrogenase, 2-methyl-4(or 5)-octanoldehydrogenase, 8-methyl-4(or 5)-nonanol dehydrogenase, 1-phenyl-2(or3)-hexanol dehydrogenase, 1-(4-hydroxyphenyl)-2(or 3)-hexanoldehydrogenase, 1-indole-2(or 3)-hexanol dehydrogenase, 4(or 5)-undecanoldehydrogenase, 5(or 6)-undecanol dehydrogenase, 5(or 6)-tridecanoldehydrogenase, 2-methyl-3(or 4)-octanol dehydrogenase, 3-methyl-4(or5)-nonanol dehydrogenase, 2-methyl-4(or 5)-nonanol dehydrogenase,2-methyl-5(or 6)-decanol dehydrogenase, 1-phenyl-2(or 3)-heptanoldehydrogenase, 1-(4-hydroxyphenyl)-2(or 3)-heptanol dehydrogenase,1-indole-2(or 3)-heptanol dehydrogenase, 6(or 7)-tridecanoldehydrogenase, 6(or 7)-tetradecanol dehydrogenase, 2-methyl-3(or4)-nonanol dehydrogenase, 3-methyl-4(or 5)-decanol dehydrogenase,2-methyl-4(or 5)-decanol dehydrogenase, 2-methyl-5(or 6)-undecanoldehydrogenase, 1-phenyl-2(or 3)-octanol dehydrogenase,1-(4-hydroxyphenyl)-2(or 3)-octanol dehydrogenase, 1-indole-2(or3)-octanol dehydrogenase, 7(or 8)-pentadecanol dehydrogenase,2-methyl-3(or 4)-decanol dehydrogenase, 3-methyl-4(or 5)-undecanoldehydrogenase, 2-methyl-4(or 5)-undecanol dehydrogenase, 2-methyl-5 (or6)-dodecanol dehydrogenase, 1-phenyl-2(or 3)-nonanol dehydrogenase,1-(4-hydroxyphenyl)-2 (or 3)-nonanol dehydrogenase, 1-indole-2(or3)-nonanol dehydrogenase, 2-methyl-3(or 4)-undecanol dehydrogenase,3-methyl-4(or 5)-dodecanol dehydrogenase, 2-methyl-4(or 5)-dodecanoldehydrogenase, 2-methyl-5(or 6)-tridecanol dehydrogenase, 1-phenyl-2(or3)-decanol dehydrogenase, 1-(4-hydroxyphenyl)-2 (or 3)-decanoldehydrogenase, 1-indole-2(or 3)-decanol dehydrogenase, 2,5-dimethyl-3(or4)-heptanol dehydrogenase, 2,6-dimethyl-3(or 4)-heptanol dehydrogenase,2,7-dimethyl-3(or 4)-octanol dehydrogenase, 1-phenyl-4-methyl-2(or3)-pentanol dehydrogenase, 1-(4-hydroxyphenyl)-4-methyl-2(or 3)-pentanoldehydrogenase, 1-indole-4-methyl-2(or 3)-pentanol dehydrogenase,2,6-dimethyl-4(or 5)-octanol dehydrogenase, 3,8-dimethyl-4(or 5)-nonanoldehydrogenase, 1-phenyl-4-methyl-2(or 3)-hexanol dehydrogenase,1-(4-hydroxyphenyl)-4-methyl-2 (or 3)-hexanol dehydrogenase,1-indole-4-methyl-2(or 3)-hexanol dehydrogenase, 2,8-dimethyl-4(or5)-nonanol dehydrogenase, 1-phenyl-5-methyl-2(or 3)-hexanoldehydrogenase, 1-(4-hydroxyphenyl)-5-methyl-2(or 3)-hexanoldehydrogenase, 1-indole-5-methyl-2(or 3)-hexanol dehydrogenase,1-phenyl-6-methyl-2(or 3)-heptanol dehydrogenase,1-(4-hydroxyphenyl)-6-methyl-2(or 3)-heptanol dehydrogenase,1-indole-6-methyl-2(or 3)-heptanol dehydrogenase,1-(4-hydroxyphenyl)-4-phenyl-2(or 3)-butanol dehydrogenase,1-indole-4-phenyl-2(or 3)-butanol dehydrogenase,1-indole-4-(4-hydroxyphenyl)-2(or 3)-butanol dehydrogenase,1,10-diamino-5-decanol dehydrogenase, 1,4-di(4-hydroxyphenyl)-2-butanoldehydrogenase, 2-hexanol-1,6-dicarboxylic acid dehydrogenase,phenylethanol dehydrogenase, 4-hydroxyphenylethanol dehydrogenase,Indole-3-ethanol dehydrogenase, and the like.

In certain aspects, a selected alcohol dehydrogenase or secondaryalcohol dehydrogenase may have one or more of the above exemplifiedalcohol dehydrogenase activities, such as a 2-butanol dehydrogenaseactivity, 3-hexanol dehydrogenase activity, and/or a 4-octanoldehydrogenase activity, among others.

In certain aspects, a recombinant microorganism may comprise one or moresecondary alcohol dehydrogenases encoded by a nucleotide referencesequence selected from SEQ ID NO:109, 111, 113, 115, 117, 119, 121, 123,125, 127, 129, 131, 133, 135, 137, 139, and 141, or an enzyme having apolyeptide sequence selected from SEQ ID NO:110, 112, 114, 116, 118,120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, and 142,including biologically active fragments or variants thereof, such asoptimized variants. Certain aspects may also comprises nucleotidesequences or polypeptide sequences having 80%, 85%, 90%, 95%, 97%, 98%,99% sequence identity to SEQ ID NOS:109-142.

For the secondary alcohol dehydrogenase sequences referred to above, SEQID NO:109 is the nucleotide sequence and SEQ ID NO:110 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-1:PP_(—)1946) isolated from Pseudomonas putida KT2440. SEQ ID NO:111 isthe nucleotide sequence and SEQ ID NO:112 is the polypeptide sequence ofa secondary alcohol dehydrogenase (2adh-2: PP_(—)1817) isolated fromPseudomonas putida KT2440.

SEQ ID NO:113 is the nucleotide sequence and SEQ ID NO:114 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-3:PP_(—)1953) isolated from Pseudomonas putida KT2440. SEQ ID NO:115 isthe nucleotide sequence and SEQ ID NO:116 is the polypeptide sequence ofa secondary alcohol dehydrogenase (2adh-4: PP_(—)3037) isolated fromPseudomonas putida KT2440.

SEQ ID NO:117 is the nucleotide sequence and SEQ ID NO:118 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-5:PP_(—)1852) isolated from Pseudomonas putida KT2440. SEQ ID NO:119 isthe nucleotide sequence and SEQ ID NO:120 is the polypeptide sequence ofa secondary alcohol dehydrogenase (2adh-6: PP_(—)2723) isolated fromPseudomonas putida KT2440.

SEQ ID NO:121 is the nucleotide sequence and SEQ ID NO:122 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-7:PP_(—)2002) isolated from Pseudomonas putida KT2440. SEQ ID NO:123 isthe nucleotide sequence and SEQ ID NO:124 is the polypeptide sequence ofa secondary alcohol dehydrogenase (2adh-8: PP_(—)1914) isolated fromPseudomonas putida KT2440.

SEQ ID NO:125 is the nucleotide sequence and SEQ ID NO:126 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-9:PP_(—)1914) isolated from Pseudomonas putida KT2440. SEQ ID NO:127 isthe nucleotide sequence and SEQ ID NO:128 is the polypeptide sequence ofa secondary alcohol dehydrogenase (2adh-10: PP_(—)3926) isolated fromPseudomonas putida KT2440.

SEQ ID NO:129 is the nucleotide sequence and SEQ ID NO:130 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-11:PFL_(—)1756) isolated from Pseudomonas fluorescens Pf-5. SEQ ID NO:131is the nucleotide sequence and SEQ ID NO:132 is the polypeptide sequenceof a secondary alcohol dehydrogenase (2adh-12: KPN_(—)01694) isolatedfrom Klebsiella pneumoniae subsp. pneumoniae MGH 78578.

SEQ ID NO:133 is the nucleotide sequence and SEQ ID NO:134 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-13:KPN_(—)02061) isolated from Kiebsiella pneumoniae subsp. pneumoniae MGH78578. SEQ ID NO:135 is the nucleotide sequence and SEQ ID NO:136 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-14:KPN_(—)00827) isolated from Klebsiella pneumoniae subsp. pneumoniae MGH78578.

SEQ ID NO:137 is the nucleotide sequence and SEQ ID NO:138 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-16:KPN_(—)01350) isolated from Kiebsiella pneumoniae subsp. pneumoniae MGH78578. SEQ ID NO:139 is the nucleotide sequence and SEQ ID NO:140 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-17:KPN_(—)03369) isolated from Klebsiella pneumoniae subsp. pneumoniae MGH78578. SEQ ID NO:141 is the nucleotide sequence and SEQ ID NO:142 is thepolypeptide sequence of a secondary alcohol dehydrogenase (2adh-18:KPN_(—)03363) isolated from Klebsiella pneumoniae subsp. pneumoniae MGH78578.

In certain aspects, an alcohol dehydrogenase (e.g., DEHU hydrogenase), asecondary alcohol dehydrogenase (2ADH), a fragment, variant, orderivative thereof, or any other enzyme that utilizes such an activesite, may comprise at least one of a nicotinamide adenine dinucleotide(NAD+), NADH, nicotinamide adenine dinucleotide phosphate (NADP+), orNADPH binding motif. In certain embodiments, the NAD+, NADH, NADP+, orNADPH binding motif may be selected from the group consisting ofY-X-G-G-X-Y, Y-X-X-G-G-X-Y, Y-X-X-X-G-G-X-Y, Y-X-G-X-X-Y,Y-X-X-G-G-X-X-Y, Y-X-X-X-G-X-X-Y, Y-X-G-X-Y, Y-X-X-G-X-Y, Y-X-X-X-G-X-Y,and Y-X-X-X-X-G-X-Y; wherein Y is independently selected from alanine,glycine, and serine, wherein G is glycine, and wherein X isindependently selected from a genetically encoded amino acid.

As one example of a step in a reduction and dehydration pathway,α-hydroxy cyclopentanone may be reduced to 1,2-cyclopentanediol. Forexample, the glycerol dehydrogenase isolated from Hansenula ofunaensisfavors the reduction of α-hydroxy ketones and α-keto ketones, and hasvery broad substrate specificity. The similar alcohol dehydrogenasederived from Hansenula polumorpha and meso-2,3-butanediol dehydrogenasehas similar properties. Certain embodiments may incorporate a1,2-cyclopentanediol dehydrogenase to the microbial system or isolatedmicroorganism. Other embodiments may incorporate a glyceroldehydrogenase from Hansenula ofunaensis, Hansenula polumorpha,Klebsiella pneumonia, or any other suitable organism.

By way of example, a chemical or hydrocarbon such as1,2-cyclopentanediol may be dehydrated to form cyclopentanone as oneenzymatic step in a reduction and dehydration pathway. There are atleast two different types of diol dehydratases that may catalyzedehydration of chemicals such as 1,2-cyclopentanediol. Certainembodiments of microbial system comprising a reduction and dehydrationpathway will comprise diol dehydratases such as 1,2-cyclopentanedioldehydratase.

In the last enzymatic step for a reduction and dehydration pathway, theconversion of such exemplary chemicals as α-hydroxy cyclopentanone tocyclopentanol may include the reduction of cyclopentanone tocyclopentanol. This step may be catalyzed by cyclopentanoldehydrogenase, which is found in Comomonas sp. strain NCIMB 9872 and itsgene (cpnA) has been isolated. Certain embodiments of a microbial systemor isolated microorganism may comprise a cyclopentanol dehydrogenase,such as that expressed by cpnA in Comomonas sp. strain NCIMB 9872, amongothers described herein.

As detailed below, in certain embodiments, selected C—C ligationpathways may be utilized in combination with selected components orenzymes of a reduction and dehydration pathway to produce a commoditychemical, or intermediate thereof.

For example, certain embodiments include a method wherein the C—Cligation pathway may comprise an acetoaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a2,3-butanediol dehydrogenase, a 2,3-butanediol dehydratase, and a2-butanol dehydrogenase. Additional embodiments include a method whereinthe C—C ligation pathway may comprise a propionaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 3,4-hexanediol dehydrogenase, a 3,4-hexanediol dehydratase, and a3-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 4,5-octanedioldehydrogenase, a 4,5-octanediol dehydratase, and a 4-octanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise a butyraldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a5,6-decanediol dehydrogenase, a 5,6-decanediol dehydratase, and a5-decanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 6,7-dodecanedioldehydrogenase, a 6,7-dodecanediol dehydratase, and a 6-dodecanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise a butyraldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a7,8-tetradecanediol dehydrogenase, a 7,8-tetradecanediol dehydratase,and a 7-tetradecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 8,9-hexadecanedioldehydrogenase, a 8,9-hexadecanediol dehydratase, and a 8-hexadecanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise an isobutyraldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a2,5-dimethyl-3,4-hexanediol dehydrogenase, a 2,5-dimethyl-3,4-hexanedioldehydratase, and a 2,5-dimethyl-3-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a 2-methyl-butyraldehyde lyase and wherein the reductionand dehydration pathway may comprise at least one of a3,6-dimethyl-4,5-octanediol dehydrogenase, a 3,6-dimethyl-4,5-octanedioldehydratase, and a 3,6-dimethyl-4-octanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise a 3-methyl-butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2,7-dimethyl-4,5-octanediol dehydrogenase, a 2,7-dimethyl-4,5-octanedioldehydratase, and a 2,7-dimethyl-4-octanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a 3-methyl-butyraldehyde lyase and wherein the reductionand dehydration pathway may comprise at least one of a2,9-dimethyl-5,6-decanediol dehydrogenase, a 2,9-dimethyl-4,5-decanedioldehydratase, and a 2,9-dimethyl-4-decanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise a phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1,4-diphenyl-2,3-butanediol dehydrogenase, a 1,4-diphenyl-2,3-butanedioldehydratase, and a 1,4-diphenyl-2-butanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of abis-1,4-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase, abis-1,4-(4-hydroxyphenyl)-2,3-butanediol dehydratase, and abis-1,4-(4-hydroxyphenyl)-2-butanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise a phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1,4-diindole-2,3-butanediol dehydrogenase, a 1,4-diindole-2,3-butanedioldehydratase, and a 1,4-diindole-2-butanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise an α-keto adipate carboxylyase, and wherein the reductionand dehydration pathway may comprise at least one of a1,2-cyclopentanediol dehydrogenase, a 1,2-cyclopentanediol dehydratase,and a cyclopentanol dehydrogenase. Additional embodiments include amethod wherein the C—C ligation pathway may comprise at least one of anacetoaldehyde/propiondehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 2,3-pentanedioldehydrogenase, a 2,3-pentanediol dehydratase, and a 2(or 3)-pentanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/butyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2,3-hexanediol dehydrogenase, a 2,3-hexanediol dehydratase, and a2(or 3)-hexanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of anacetoaldehyde/pentaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 2,3-heptanedioldehydrogenase, a 2,3-heptanediol dehydratase, and a 2(or 3)-heptanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/hexyldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2,3-octanediol dehydrogenase, a 2,3-octanediol dehydratase, and a2(or 3)-octanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of anacetoaldehyde/octaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 2,3-nonanedioldehydrogenase, a 2,3-nonanediol dehydratase, and a 2(or 3)-nonanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/isobutyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 4-methyl-2,3-pentanediol dehydrogenase, a 4-methyl-2,3-pentanedioldehydratase, and a 4-methyl-2(or 3)-pentanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of an acetoaldehyde/2-methyl-butyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 4-methyl-2,3-hexanediol dehydrogenase, a4-methyl-2,3-hexanediol dehydratase, and a 4-methyl-2(or 3)-hexanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/3-methyl-butyraldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 5-methyl-2,3-hexanediol dehydrogenase, a5-methyl-2,3-hexanediol dehydrogenase, and a 5-methyl-2(or 3)-hexanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of anacetoaldehyde/4-methyl-pentaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a6-methyl-2,3-heptanediol dehydrogenase, a 6-methyl-2,3-heptanedioldehydrogenase, and a 6-methyl-2(or 3)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/phenylacetaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 1-phenyl-2,3-butanediol dehydrogenase, a1-phenyl-2,3-butanediol dehydratase, and a 1-phenyl-2(or 3)-butanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of anacetoaldehyde/4-hydroxyphenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-butanediol dehydratase, and a1-(4-hydroxyphenyl)-2(or 3)-butanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an acetoaldehyde/indoleacetaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 1-indole-2,3-butanediol dehydrogenase, a1-indole-2,3-butanediol dehydratase, and a 1-indole-2(or 3)-butanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apropionaldehyde/butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 3,4-heptanedioldehydrogenase, a 3,4-heptanediol dehydratase, and a 3(or 4)-heptanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde/pentaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 3,4-octanediol dehydrogenase, a 3,4-octanediol dehydratase, and a3(or 4)-octanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of apropionaldehyde/hexyldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 3,4-nonanedioldehydrogenase, a 3,4-nonanediol dehydratase, and a 3(or 4)-nonanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde/heptaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 3,4-decanediol dehydrogenase, a 3,4-decanediol dehydratase, and a3(or 4)-decanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of apropionaldehyde/octaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 3,4-undecanedioldehydrogenase, a 3,4-undecanediol dehydratase, and a 3(or 4)-undecanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde/isobutyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 2-methyl-3,4-hexanediol dehydrogenase, a2-methyl-3,4-hexanediol dehydratase, and a 2-methyl-3(or 4)-hexanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apropionaldehyde/2-methyl-butyraldehyde lyase and wherein the reductionand dehydration pathway may comprise at least one of a5-methyl-3,4-heptanediol dehydrogenase, a 5-methyl-3,4-heptanedioldehydratase, and a 5-methyl-3 (or 4)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde/3-methyl-butyraldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 6-methyl-3,4-heptanediol dehydrogenase, a6-methyl-3,4-heptanediol dehydratase, and a 6-methyl-3(or 4)-heptanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apropionaldehyde/4-methyl-pentaldehyde lyase and wherein the reductionand dehydration pathway may comprise at least one of a7-methyl-3,4-octanediol dehydrogenase, a 7-methyl-3,4-octanedioldehydratase, and a 7-methyl-3(or 4)-octanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde and a phenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-phenyl-2,3-pentanediol dehydrogenase, a1-phenyl-2,3-pentanediol dehydratase, and a 1-phenyl-2(or 3)-pentanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apropionaldehyde/4-hydroxyphenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-(4-hydroxyphenyl)-2,3-pentanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-pentanediol dehydratase, and a1-(4-hydroxyphenyl)-2(or 3)-pentanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a propionaldehyde/indoleacetoaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 1-indole-2,3-pentanediol dehydrogenase, a1-indole-2,3-pentanediol dehydratase, and a 1-indole-2(or 3)-pentanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of abutyraldehyde/pentaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 4,5-nonanedioldehydrogenase, a 4,5-nonanediol dehydratase, and a 4(or 5)-nonanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/hexyldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 4,5-decanediol dehydrogenase, a 4,5-decanediol dehydratase, and a4(or 5)-decanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of abutyraldehyde/heptaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 4,5-undecanedioldehydrogenase, a 4,5-undecanediol dehydratase, and a 4(or 5)-undecanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/octaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 4,5-dodecanediol dehydrogenase, a 4,5-dodecanediol dehydratase, anda 4(or 5)-dodecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/isobutyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2-methyl-3,4-heptanediol dehydrogenase, a 2-methyl-3,4-heptanedioldehydratase, and a 2-methyl-3(or 4)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/2-methyl-butyraldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 3-methyl-4,5-octanediol dehydrogenase, a3-methyl-4,5-octanediol dehydratase, and a 3-methyl-4(or 5)-octanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of abutyraldehyde/3-methyl-butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-4,5-octanediol dehydrogenase, a 2-methyl-4,5-octanedioldehydratase, and a 2-methyl-4(or 5)-octanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/4-methyl-pentaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of an 8-methyl-4,5-nonanediol dehydrogenase, an8-methyl-4,5-nonanediol dehydratase, and an 8-methyl-4(or 5)-nonanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of abutyraldehyde/phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1-phenyl-2,3-hexanediol dehydrogenase, a 1-phenyl-2,3-hexanedioldehydratase, and a 1-phenyl-2(or 3)-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a butyraldehyde/4-hydroxyphenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-(4-hydroxyphenyl)-2,3-hexanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-hexanediol dehydratase, and a1-(4-hydroxyphenyl)-2(or 3)-hexanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a butyraldehyde/indoleacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-indole-2,3-hexanediol dehydrogenase, a 1-indole-2,3-hexanedioldehydratase, and a 1-indole-2(or 3)-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a pentaldehyde/hexyldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 5,6-undecanediol dehydrogenase, a 4,5-undecanediol dehydratase, anda 4(or 5)-undecanol dehydrogenase. Additional embodiments include amethod wherein the C—C ligation pathway may comprise at least one of apentaldehyde/heptaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a 5,6-undecanedioldehydrogenase, a 5,6-undecanediol dehydratase, and a 5(or 6)-undecanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a pentaldehyde/octaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 5,6-tridecanediol dehydrogenase, a 5,6-tridecanediol dehydratase,and a 5(or 6)-tridecanol dehydrogenase. Additional embodiments include amethod wherein the C—C ligation pathway may comprise at least one of apentaldehyde/isobutyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-3,4-octanediol dehydrogenase, a 2-methyl-3,4-octanedioldehydratase, and a 2-methyl-3(or 4)-octanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a pentaldehyde/2-methyl-butyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 3-methyl-4,5-nonanediol dehydrogenase, a3-methyl-4,5-nonanediol dehydratase, and a 3-methyl-4(or 5)-nonanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apentaldehyde/3-methyl-butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-4,5-nonanediol dehydrogenase, a 2-methyl-4,5-nonanedioldehydratase, and a 2-methyl-4(or 5)-nonanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a pentaldehyde/4-methyl-pentaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 2-methyl-5,6-decanediol dehydrogenase, a2-methyl-5,6-decanediol dehydratase, and a 2-methyl-5(or 6)-decanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of apentaldehyde/phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1-phenyl-2,3-heptanediol dehydrogenase, a 1-phenyl-2,3-heptanedioldehydratase, and a 1-phenyl-2(or 3)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a pentaldehyde/4-hydroxyphenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-(4-hydroxyphenyl)-2,3-heptanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-heptanediol dehydratase, and a1-(4-hydroxyphenyl)-2(or 3)-heptanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a pentaldehyde/indoleacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-indole-2,3-heptanediol dehydrogenase, a 1-indole-2,3-heptanedioldehydratase, and a 1-indole-2(or 3)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a hexyldehyde/heptaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 6,7-tridecanediol dehydrogenase, a 6,7-tridecanediol dehydratase,and a 6(or 7)-tridecanol dehydrogenase. Additional embodiments include amethod wherein the C—C ligation pathway may comprise at least one of ahexyldehyde/octaldehyde lyase and wherein the reduction and dehydrationpathway may comprise at least one of a 6,7-tetradecanedioldehydrogenase, a 6,7-tetradecanediol dehydratase, and a 6(or7)-tetradecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a hexyldehyde/isobutyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2-methyl-3,4-nonanediol dehydrogenase, a 2-methyl-3,4-nonanedioldehydratase, and a 2-methyl-3(or 4)-nonanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a hexyldehyde/2-methyl-butyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 3-methyl-4,5-decanediol dehydrogenase, a 3-methyl-4,5-decanedioldehydratase, and a 3-methyl-4(or 5)-decanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a hexyldehyde/3-methyl-butyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 2-methyl-4,5-decanediol dehydrogenase, a2-methyl-4,5-decanediol dehydratase, and a 2-methyl-4(or 5)-decanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of ahexyldehyde/4-methyl-pentaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-5,6-undecanediol dehydrogenase, a 2-methyl-5,6-undecanedioldehydratase, and a 2-methyl-5(or 6)-undecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a hexyldehyde/phenylacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-phenyl-2,3-octanediol dehydrogenase, a 1-phenyl-2,3-octanedioldehydratase, and a 1-phenyl-2(or 3)-octanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a hexyldehyde/4-hydroxyphenylacetaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 1-(4-hydroxyphenyl)-2,3-octanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-octanediol dehydratase, and a1-(4-hydroxyphenyl)-2(or 3)-octanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a hexyldehyde/indoleacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-indole-2,3-octanediol dehydrogenase, a 1-indole-2,3-octanedioldehydratase, and a 1-indole-2(or 3)-octanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a heptaldehyde/octaldehyde lyase and whereinthe reduction and dehydration pathway may comprise at least one of a7,8-pentadecanediol dehydrogenase, a 7,8-pentadecanediol dehydratase,and a 7(or 8)-pentadecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a heptaldehyde/isobutyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2-methyl-3,4-decanediol dehydrogenase, a 2-methyl-3,4-decanedioldehydratase, and a 2-methyl-3(or 4)-decanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a heptaldehyde/2-methyl-butyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 3-methyl-4,5-undecanediol dehydrogenase, a3-methyl-4,5-undecanediol dehydratase, and a 3-methyl-4(or 5)-undecanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a heptaldehyde/3-methyl-butyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 2-methyl-4,5-undecanediol dehydrogenase, a2-methyl-4,5-undecanediol dehydratase, and a 2-methyl-4(or 5)-undecanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of aheptaldehyde/4-methyl-pentaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-5,6-dodecanediol dehydrogenase, a 2-methyl-5,6-dodecanedioldehydratase, and a 2-methyl-5(or 6)-dodecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a heptaldehyde/phenylacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-phenyl-2,3-nonanediol dehydrogenase, a 1-phenyl-2,3-nonanedioldehydratase, and a 1-phenyl-2(or 3)-nonanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a heptaldehyde/4-hydroxyphenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-(4-hydroxyphenyl)-2,3-nonanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-nonanediol dehydratase, and a1-(4-hydroxyphenyl)-2 (or 3)-nonanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a heptaldehyde/indoleacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-indole-2,3-nonanediol dehydrogenase, a 1-indole-2,3-nonanedioldehydratase, and a 1-indole-2(or 3)-nonanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of an octaldehyde/isobutyraldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 2-methyl-3,4-undecanediol dehydrogenase, a2-methyl-3,4-undecanediol dehydratase, and a 2-methyl-3(or 4)-undecanoldehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an octaldehyde/2-methyl-butyraldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 3-methyl-4,5-dodecanediol dehydrogenase, a3-methyl-4,5-dodecanediol dehydratase, and a 3-methyl-4(or 5)-dodecanoldehydrogenase. Additional embodiments include a method wherein the C—Cligation pathway may comprise at least one of anoctaldehyde/3-methyl-butyraldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a2-methyl-4,5-dodecanediol dehydrogenase, a 2-methyl-4,5-dodecanedioldehydratase, and a 2-methyl-4(or 5)-dodecanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an octaldehyde/4-methyl-pentaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 2-methyl-5,6-tridecanediol dehydrogenase, a2-methyl-5,6-tridecanediol dehydratase, and a 2-methyl-5(or6)-tridecanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of anoctaldehyde/phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1-phenyl-2,3-decanediol dehydrogenase, a 1-phenyl-2,3-decanedioldehydratase, and a 1-phenyl-2(or 3)-decanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an octaldehyde/4-hydroxyphenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-(4-hydroxyphenyl)-2,3-decanediol dehydrogenase, a1-(4-hydroxyphenyl)-2,3-decanediol dehydratase, and a1-(4-hydroxyphenyl)-2 (or 3)-decanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of an octaldehyde/indoleacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-indole-2,3-decanediol dehydrogenase, a 1-indole-2,3-decanedioldehydratase, and a 1-indole-2(or 3)-decanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an isobutyraldehyde/2-methyl-butyraldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 2,5-dimethyl-3,4-heptanediol dehydrogenase, a2,5-dimethyl-3,4-heptanediol dehydratase, and a 2,5-dimethyl-3(or4)-heptanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of anisobutyraldehyde/3-methyl-butyraldehyde lyase and wherein the reductionand dehydration pathway may comprise at least one of a2,6-dimethyl-3,4-heptanediol dehydrogenase, a2,6-dimethyl-3,4-heptanediol dehydratase, and a 2,6-dimethyl-3(or4)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of an isobutyraldehyde/4-methyl-pentaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 2,7-dimethyl-3,4-octanediol dehydrogenase, a2,7-dimethyl-3,4-octanediol dehydratase, and a 2,7-dimethyl-3(or4)-octanol dehydrogenase. Additional embodiments include a methodwherein the C—C ligation pathway may comprise at least one of anisobutyraldehyde/phenylacetaldehyde lyase and wherein the reduction anddehydration pathway may comprise at least one of a1-phenyl-4-methyl-2,3-pentanediol dehydrogenase, a1-phenyl-4-methyl-2,3-pentanediol dehydratase, and a1-phenyl-4-methyl-2(or 3)-pentanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of anisobutyraldehyde/4-hydroxyphenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-(4-hydroxyphenyl)-4-methyl-2,3-pentanediol dehydrogenase, a1-(4-hydroxyphenyl)-4-methyl-2,3-pentanediol dehydratase, and a1-(4-hydroxyphenyl)-4-methyl-2(or 3)-pentanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of an isobutyraldehyde/indoleacetaldehyde lyaseand wherein the reduction and dehydration pathway may comprise at leastone of a 1-indole-4-methyl-2,3-pentanediol dehydrogenase, a1-indole-4-methyl-2,3-pentanediol dehydratase, and a1-indole-4-methyl-2(or 3)-pentanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a2-methyl-butyraldehyde/3-methyl-butyraldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a2,6-dimethyl-4,5-octanediol dehydrogenase, a 2,6-dimethyl-4,5-octanedioldehydratase, and a 2,6-dimethyl-4(or 5)-octanol dehydrogenase.Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a2-methyl-butyraldehyde/4-methyl-pentaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a3,8-dimethyl-4,5-nonanediol dehydrogenase, a 3,8-dimethyl-4,5-nonanedioldehydratase, and a 3,8-dimethyl-4(or 5)-nonanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a 2-methyl-butyraldehyde/phenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-phenyl-4-methyl-2,3-hexanediol dehydrogenase, a1-phenyl-4-methyl-2,3-hexanediol dehydratase, and a1-phenyl-4-methyl-2(or 3)-hexanol dehydrogenase. Additional embodimentsinclude a method wherein the C—C ligation pathway may comprise at leastone of a 2-methyl-butyraldehyde/4-hydroxyphenylacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-(4-hydroxyphenyl)-4-methyl-2,3-hexanediol dehydrogenase, a1-(4-hydroxyphenyl)-4-methyl-2,3-hexanediol dehydratase, and a1-(4-hydroxyphenyl)-4-methyl-2 (or 3)-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a 2-methyl-butyraldehyde/indoleacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-indole-4-methyl-2,3-hexanediol dehydrogenase, a1-indole-4-methyl-2,3-hexanediol dehydratase, and a1-indole-4-methyl-2(or 3)-hexanol dehydrogenase. Additional embodimentsinclude a method wherein the C—C ligation pathway may comprise at leastone of a 3-methyl-butyraldehyde/4-methyl-pentaldehyde lyase and whereinthe reduction and dehydration pathway may comprise at least one of a2,8-dimethyl-4,5-nonanediol dehydrogenase, a 2,8-dimethyl-4,5-nonanedioldehydratase, and a 2,8-dimethyl-4(or 5)-nonanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a 3-methyl-butyraldehyde/phenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-phenyl-5-methyl-2,3-hexanediol dehydrogenase, a1-phenyl-5-methyl-2,3-hexanediol dehydratase, and a1-phenyl-5-methyl-2(or 3)-hexanol dehydrogenase. Additional embodimentsinclude a method wherein the C—C ligation pathway may comprise at leastone of a 3-methyl-butyraldehyde/4-hydroxyphenylacetaldehyde lyase andwherein the reduction and dehydration pathway may comprise at least oneof a 1-(4-hydroxyphenyl)-5-methyl-2,3-hexanediol dehydrogenase, a1-(4-hydroxyphenyl)-5-methyl-2,3-hexanediol dehydratase, and a1-(4-hydroxyphenyl)-5-methyl-2(or 3)-hexanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a 3-methyl-butyraldehyde/indoleacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-indole-5-methyl-2,3-hexanediol dehydrogenase, a1-indole-5-methyl-2,3-hexanediol dehydratase, and a1-indole-5-methyl-2(or 3)-hexanol dehydrogenase. Additional embodimentsinclude a method wherein the C—C ligation pathway may comprise at leastone of a 4-methyl-pentaldehyde/phenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-phenyl-6-methyl-2,3-heptanediol dehydrogenase, a1-phenyl-6-methyl-2,3-heptanediol dehydratase, and a1-phenyl-6-methyl-2(or 3)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a4-methyl-pentaldehyde/4-hydroxyphenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-(4-hydroxyphenyl)-6-methyl-2,3-heptanediol dehydrogenase, a1-(4-hydroxyphenyl)-6-methyl-2,3-heptanediol dehydratase, and a1-(4-hydroxyphenyl)-6-methyl-2(or 3)-heptanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a 4-methyl-pentaldehyde/Indoleacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-indole-6-methyl-2,3-heptanediol dehydrogenase, a1-indole-6-methyl-2,3-heptanediol dehydratase, and a1-indole-6-methyl-2(or 3)-heptanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of aphenylacetaldehyde/4-hydroxyphenylacetaldehyde lyase and wherein thereduction and dehydration pathway may comprise at least one of a1-(4-hydroxyphenyl)-4-phenyl-2,3-butanediol dehydrogenase, a1-(4-hydroxyphenyl)-4-phenyl-2,3-butanediol dehydratase, and a1-(4-hydroxyphenyl)-4-phenyl-2(or 3)-butanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise at least one of a phenylacetaldehyde/indolephenylacetaldehydelyase and wherein the reduction and dehydration pathway may comprise atleast one of a 1-indole-4-phenyl-2,3-butanediol dehydrogenase, a1-indole-4-phenyl-2,3-butanediol dehydratase, and a1-indole-4-phenyl-2(or 3)-butanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise at least one of a4-hydroxyphenylacetaldehyde/indolephenylacetaldehyde lyase and whereinthe reduction and dehydration pathway may comprise at least one of a1-indole-4-(4-hydroxyphenyl)-2,3-butanediol dehydrogenase, a1-indole-4-(4-hydroxyphenyl)-2,3-butanediol dehydratase, and a1-indole-4-(4-hydroxyphenyl)-2(or 3)-butanol dehydrogenase. Additionalembodiments include a method wherein the C—C ligation pathway maycomprise a 5-amino-pantaldehyde lyase, and wherein the reduction anddehydration pathway may comprise at least one of a1,10-diamino-5,6-decanediol dehydrogenase, a 1,10-diamino-5,6-decanedioldehydratase, and a 1,10-diamino-5-decanol dehydrogenase.

Additional embodiments include a method wherein the C—C ligation pathwaymay comprise a 4-hydroxyphenyl acetaldehyde lyase, and wherein thereduction and dehydration pathway may comprise at least one of a1,4-di(4-hydroxyphenyl)-2,3-butanediol, a1,4-di(4-hydroxyphenyl)-2,3-butanediol dehydratase, and a1,4-di(4-hydroxyphenyl)-2-butanol dehydrogenase. Additional embodimentsinclude a method wherein the C—C ligation pathway may comprise asuccinate semialdehyde lyase, and wherein the reduction and dehydrationpathway may comprise at least one of a 2,3-hexanediol-1,6-dicarboxylicacid dehydrogenase, a 2,3-hexanediol-1,6-dicarboxylic acid dehydratase,and a 2-hexanol-1,6-dicarboxylic dehydrogenase.

Certain embodiments of a microbial system or recombinant microorganismmay comprise genes encoding enzymes that are able to catalyze (e.g.,reduction and dehydration) the conversion of 4-octanol to octene oroctane. Other embodiments may comprise redesigned or de novo designedenzymes for this reduction and dehydration pathway. For example, threeredesigned enzymes could convert 4-octanone to either 3- and 4-octene.The first step could be catalyzed by redesigned isocitratedehydrogenase. This enzyme could catalyze the formation of4-hydroxy-3(or 5)-carboxylic octane. The 4-hydroxy group could bephosphorylated by redesigned kinase. Finally, redesigned mevalonatediphosphate decarboxylase catalyzes the formation of 3(or 4)-octene.

In other embodiments, several redesigned enzymes could convert4-octanone to octane. For example, the 4-hydroxy-3(or 5)-carboxylicoctane is sequentially reduced and dehydrated to form 3(or 5)-carboxylicoctane. Redesigned enzymes involved in fatty acid metabolism cancatalyze these reactions. The 3(or 5)-carboxylic octane can be reducedto corresponding aldehyde by aldehyde dehydrogenase and the product maybe decarbonylated to form octane catalyzed by a redesigneddecarbonylase.

As noted above, for the production of certain commodity chemicals, suchas 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and indole-3-ethanol,among other similar chemicals, a biosynthesis pathway (e.g., aldehydebiosynthesis pathway) may optionally or further comprise one or moregenes encoding a decarboxylase enzyme, such as an indole-3-pyruvatedecarboxylase (IPDC), to produce an aldehyde. In certain aspects, anIPDC may comprise an amino acid sequence that is at least 80%, 90%, 95%,98%, or 99% identical to the amino acid sequence set forth in SEQ IDNO:312. An IDPC enzyme may comprise certain conserved amino acidresidues, such as G24, D25, E48, A55, R60, G75, E89, H113, G252, G405,G413, G428, G430, and/or N456.

In these and other embodiments, a recombinant microorganism may comprisean aldehyde reductase, such as a phenylacetoaldehyde reductase (PAR), toconvert an aldehyde to a commodity chemical. In certain aspects, a PARmay comprise an amino acid sequence that is at least 80%, 90%, 95%, 98%,or 99% identical to the amino acid sequence set forth in SEQ ID NO:313,which shows the sequence of a PAR enzymed derived from Rhodococcus sp.ST-10. In certain aspects, a PAR enzyme may comprise at least one of anicotinamide adenine dinucleotide (NAD+), NADH, nicotinamide adeninedinucleotide phosphate (NADP+), or NADPH binding motif. In certainembodiments, the NAD+, NADH, NADP+, or NADPH binding motif may beselected from the group consisting of Y-X-G-G-X-Y, Y-X-X-G-G-X-Y,Y-X-X-X-G-G-X-Y, Y-X-G-X-X-Y, Y-X-X-G-G-X-X-Y, Y-X-X-X-G-X-X-Y,Y-X-G-X-Y, Y-X-X-G-X-Y, Y-X-X-X-G-X-Y, and Y-X-X-X-X-G-X-Y; wherein Y isindependently selected from alanine, glycine, and serine, wherein G isglycine, and wherein X is independently selected from a geneticallyencoded amino acid.

In certain embodiments, such a recombinant microorganism may also oralternatively comprise a secondary alcohol dehydrogenase having anactivity selected from at least one of a phenylethanol dehydrogenaseactivity, a 4-hydroxyphenylethanol dehydrogenase activity, and anIndole-3-ethanol dehydrogenase activity, to reduce the aldehyde to itscorresponding alcohol (e.g. 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol,and indole-3-ethanol).

Embodiments of the present invention also include methods for convertinga suitable monosaccharide to a commodity chemical comprising, (a)obtaining a suitable monosaccharide; (b) contacting the suitablemonosaccharide with a microbial system for a time sufficient to convertto the suitable monosaccharide to the biofuel, wherein the microbialsystem comprises, (i) one or more genes encoding and expressing a fattyacid biosynthesis pathway, an amino acid biosynthetic pathway, and/or ashort chain alcohol biosynthetic pathway; (ii) one or more genesencoding and expressing a keto-acid decarboxylase, aldehydedehydrogenase, and/or alcohol dehydrogenase; and (iii) an enzymaticreduction pathway selected from (1) an enzymatic long chain alcoholreduction pathway, (2) an enzymatic decarbonylation pathway, (3) anenzymatic decarboxylation pathway, and (4) an enzymatic reductionpathway comprising (1), (2), and/or (3), thereby converting the suitablemonosaccharide to the commodity chemical.

Embodiments of the present invention may comprise one or more genesencoding and expressing enzymes in a fatty acid synthesis pathway, whichmay be used, as one example, to produce biofuels in the form of alkanes,such as medium to long chain alkanes. In certain embodiments, thespecificity of the fatty acid biosynthesis pathway in the microbialsystem may be recalibrated or redesigned. Merely by way of example,microorganisms generally produce a mixture of long chain fatty acids(e.g., E. coli naturally produce large quantities of long chain fattyacids (C16-C19: <95% in whole cells) and small quantity of medium chainfatty acids (C12: 2% and C14: 5% in whole cells)).

In certain embodiments, the recalibration or re-engineering may bedirected to increasing production of medium chain alkanes, including,but not limited to, caprylate (C8), caprate (C10), laurate (C12),myristate (C14), and palmitate (C16), as alkanes produced from thesefatty acids are major components of gasoline, diesels, and kerosene. Inaddition to these fatty acids, other embodiments may be directed toincreased production of long chain fatty acids, including, but notlimited to, stearate (C18), arachidonate (C20), behenate (C22) andlonger fatty acids, as n-alkanes produced from these fatty acids are oneof major components in heavy oils.

For example, Cuphea mainly accumulate medium chain fatty acids as majorcomponents in their seed oils, and these compositions alter depending onspecies. In particular, Cuphea pulcherrima accumulates caprylate (C8:0)96%, Cuphea koehneana accumulates caprate (C10:0) 95.3%, and Cupheapolymorpha accumulates laurate (C12:0) 80.1%. Embodiments of themicrobial systems or isolated microorganisms according to the presentapplication may incorporate genes from various Cuphea species encodingenzymes involved in a fatty acid biosynthesis pathway, and thesemicroorganisms may be directed in part to the production of middle chainfatty acids.

In other embodiments, acyl-acyl carrier protein (ACP) thioesterases(TEs) derived from various species including Cuphea hookeriana, Cupheapalustris, Umbellularia californica, and Cinnamomum camphorum may beover-expressed in such microorganisms as E. coli, wherein the specificactivity for the formation of each medium chain fatty acids, caprylate(C8), caprate (C10), laurate (C12), myristate (C14), and palmitate (C16)is improved over the wild type. Certain embodiments may include otherenzyme components involved in fatty acid biosynthesis as known to aperson skilled in the arts, including, but not limited to, ACP andβ-ketoacyl ACP synthase (KAS) IV.

Microbial systems and isolated microorganisms of the present applicationmay also incorporate fatty aldehyde dehydrogenases to reduce fatty acidsto fatty aldehydes. Merely by way of explanation, the conversion offatty acids to fatty aldehydes may be catalyzed by medium and/or longchain fatty aldehyde dehydrogenases isolated from various suitableorganisms. Certain embodiments may incorporate, for example, a fattyaldehyde dehydrogenase derived from Vibrio harveyi.

Microbial systems and isolated microorganisms of the present applicationmay also incorporate one or more enzymes that catalyze the conversion offatty aldehydes to biofuels such as n-alkanes, including, for example,enzymes comprising an enzymatic long chain alcohol reduction pathway.Certain embodiments may incorporate genes from various other sourcesthat encode enzymes capable of catalyzing the reduction and dehydrationof fatty acids to biofuels, such as alkanes. For example, bacterialstrain HD-1 is able to produce biofuels, such as n-alkanes, with variouschain lengths, and also produces both odd and even numbered alkanes.Certain embodiments of the microbial systems and recombinantmicroorganisms provided herein may incorporate the HD-1 genes encodingthe enzymes involved in this pathway.

Other embodiments may incorporate redesigned or de novo designed enzymesfor this reduction pathway. For example, embodiments of the presentinvention may include a redesigned isocitrate dehydrogenase, which maycatalyze the formation of 2-carboxy-1-alcohols. In certain embodiments,the 2-carboxy-1-alcohols may be sequentially reduced and dehydrated toform 2-carboxy-alkanes, which may be catalyzed by redesigned enzymesinvolved in fatty acid metabolism. The 2-carboxy-alkanes can be reducedto corresponding aldehyde by aldehyde dehydrogenase and thendecarbonylated to form n-alkanes catalyzed by the redesigneddecarbonylase as discussed below. Certain embodiments of these microbialsystems may produce either even numbered n-alkanes, odd numberedn-alkanes, or both.

Certain embodiments of the present application may incorporate the genesencoding enzymes catalyzing decarbonylation, or an enzymaticdecarbonylation pathway. Merely by way of example, green colonial algaBotyrococcus braunii, race A, produces linear odd-numbered C27, C29, andC31 hydrocarbons that total up to 32% of the alga's dry weight.Microsomal preparations of this organism have decarbonylation activity.This decarbonylase from B. braunii culture is a cobalt-protoporphyrin IXcontaining enzyme. Certain microbial systems of isolated microorganismsmay incorporate the gene encoding fatty aldehyde decarbonylase fromBotyrococcus braunii.

Other embodiments may include redesigned decarbonylase enzymes, forexample, wherein the N-terminal membrane sequence is substituted. By wayof explanation, the functional activity of a similar enzyme, cytochromeP450 containing Fe-protopolphyrin IX (heme), is improved by substitutingN-terminal membrane associated sequence, and the functional activity ofdecarbonylases of the present microbial systems may comprise similarsubstitutions or improvements.

Other embodiments may incorporate the genes encoding a Co-porphyrinsynthase. In explanation, decarbonylase enzymes may useCo-protoporphyrin IX as a co-factor, and Clostridium tetranomorphum isable to incorporate cobalt into incubated protopolphyrin IX. Certainembodiments may incorporate the Co-porphyrin synthase from Clostridiumtetranomorphum, or from other suitable microorganisms. Other embodimentsmay incorporate de novo designed decarbonylation enzymes using inorganicmetals such as Co²⁺, Fe²⁺, and Ni²⁺ as catalysts.

Certain embodiments may comprise genes encoding the enzymes responsiblefor the formation of alkenes, or an enzymatic decarboxylation pathway.These genes may be derived or isolated from various sources, such ashigher plants and insects. For example, higher plants such asgerminating safflower (Carthamus tinctorius L.) produce a number of oddnumbered 1-alkenes, including 1-pentadecene, 1-heptadecene,1,8-heptadecadiene and 1,8,11-heptadecatriene besides about 80-90%1,8,11,14-heptadecatetraene by decarboxylation from their correspondingfatty acids. Certain embodiments may incorporate the genes from higherplants such as Carthamus tinctorius.

Other embodiments may incorporate the genes encoding the enzymesresponsible for the formation of alkenes (e.g., an enzymaticdecarboxylation pathway) from microorganisms, including, but not limitedto, such as bacterial strain DH-1. By way of explanation, bacterialstrain DH-1 produces n-alkenes in addition to n-alkanes.

Other embodiments may incorporate the genes from de novo designedenzymes for an enzymatic decarboxylation pathway. For example, theseredesigned enzymes convert β-hydroxy fatty acids to n-alkenes. The firststep is catalyzed by a redesigned kinase, which catalyzes thephosphorylation of a β-hydroxy group. A redesigned mevalonatediphosphate decarboxylase then catalyzes the formation of n-alkenes,such as n-1-alkene.

Any microorganism may be utilized according to the present invention. Incertain aspects, a microorganism is a eukaryotic or prokaryoticmicroorganism. In certain aspects, a microrganism is a yeast, such as S.cerevisiae. In certain aspects, a microorganism is a bacteria, such as agram-positive bacteria or a gram-negative bacteria. Given its rapidgrowth rate, well-understood genetics, the variety of available genetictools, and its capability in producing heterologous proteins,genetically modified E. coli may be used in certain embodiments of amicrobial system as described herein, whether for the degradation andmetabolism of a polysaccharide, such as alginate or pectin, or theformation or biosynthesis of commodity chemicals, such as biofuels.

Other microorganisms may be used according to the present invention,based in part on the compatibility of enzymes and metabolites to hostorganisms. For example, other organisms such as Acetobacter aceti,Achromobacter, Acidiphilium, Acinetobacter, Actinomadura, Actinoplanes,Aeropyrum pernix, Agrobacterium, Alcaligenes, Ananas comosus (M),Arthrobacter, Aspargillus niger, Aspargillus oryze, Aspergillus melleus,Aspergillus pulverulentus, Aspergillus saitoi, Aspergillus sojea,Aspergillus usamii, Bacillus alcalophilus, Bacillus amyloliquefaciens,Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus lentus,Bacillus licheniformis, Bacillus macerans, Bacillus stearothermophilus,Bacillus subtilis, Bifidobacterium, Brevibacillus brevis, Burkholderiacepacia, Candida cylindracea, Candida rugosa, Carica papaya (L),Cellulosimicrobium, Cephalosporium, Chaetomium erraticum, Chaetomiumgracile, Clostridium, Clostridium butyricum, Clostridium acetobutylicum,Clostridium thermocellum, Corynebacterium (glutamicum), Corynebacteriumefficiens, Escherichia coli, Enterococcus, Erwina chrysanthemi,Gliconobacter, Gluconacetobacter, Haloarcula, Humicola insolens,Humicola nsolens, Kitasatospora setae, Klebsiella, Klebsiella oxytoca,Kluyveromyces, Kluyveromyces fragilis, Kluyveromyces lactis, Kocuria,Lactlactis, Lactobacillus, Lactobacillus fermentum, Lactobacillus sake,Lactococcus, Lactococcus lactis, Leuconostoc, Methylocystis,Methanolobus siciliae, Methanogenium organophilum, Methanobacteriumbryantii, Microbacterium imperiale, Micrococcus lysodeikticus,Microlunatus, Mucor javanicus, Mycobacterium, Myrothecium, Nitrobacter,Nitrosomonas, Nocardia, Papaya carica, Pediococcus, Pediococcushalophilus, Penicillium, Penicillium camemberti, Penicillium citrinum,Penicillium emersonii, Penicillium roqueforti, Penicillum lilactinum,Penicillum multicolor, Paracoccus pantotrophus, Propionibacterium,Pseudomonas, Pseudomonas fluorescens, Pseudomonas denitrificans,Pyrococcus, Pyrococcus furiosus, Pyrococcus horikoshii, Rhizobium,Rhizomucor miehei, Rhizomucor pusillus Lindt, Rhizopus, Rhizopusdelemar, Rhizopus japonicus, Rhizopus niveus, Rhizopus oryzae, Rhizopusoligosporus, Rhodococcus, Sccharomyces cerevisiae, Sclerotina libertina,Sphingobacterium multivorum, Sphingobium, Sphingomonas, Streptococcus,Streptococcus thermophilus Y-1, Streptomyces, Streptomyces griseus,Streptomyces lividans, Streptomyces murinus, Streptomyces rubiginosus,Streptomyces violaceoruber, Streptoverticillium mobaraense,Tetragenococcus, Thermus, Thiosphaera pantotropha, Trametes,Trichoderma, Trichoderma longibrachiatum, Trichoderma reesei,Trichoderma viride, Trichosporon penicillatum, Vibrio alginolyticus,Xanthomonas, yeast, Zygosaccharomyces rouxii, Zymomonas, and Zymomonusmobilis, may be utilized as recombinant microorganisms provided herein,and, thus, may be utilized according to the various methods of thepresent invention.

The following Examples are offered by way of illustration, notlimitation.

EXAMPLES Example 1 Engineering E. Coli to Grow on Alginate as a SoleSource of Carbon

Wild type E. coli cannot use alginate polymer or degraded alginate asits sole carbon source (see FIG. 4). Vibrio splendidus, however, isknown to be able to metabolize alginate to support growth. To generaterecombinant E. coli that use degraded alginate as its sole carbonsource, a Vibrio splendidus fosmid library was constructed and clonedinto E. coli.

To prepare the Vibrio splendidus fosmid library, genomic DNA wasisolated from Vibrio Splendidus B01 (gift from Dr. Martin Polz, MIT)using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, Calif.). Afosmid library was then constructed using Copy Control Fosmid LibraryProduction Kit (Epicentre, Madison, Wis.). This library consisted ofrandom genomic fragments of approximately 40 kb inserted into the vectorpCC1 FOS (Epicentre, Madison, Wis.).

The fosmid library was packaged into phage, and E. coli DH10B cellsharboring a pDONR221 plasmid (Invitrogen, Carlsbad, Calif.) carryingcertain Vibrio splendidus genes (V12B01_(—)02425 to V12B01_(—)02480;encoding a type II secretion apparatus; see SEQ ID NO:1) weretransfected with the phage library. This secretome region encodes a typeII secretion apparatus derived from Vibrio splendidus, which was clonedinto a pDONR221 plasmid and introduced into E. coli strain DH10B (seeExample 1).

Transformants were selected for chloroamphenicol resistance and thenscreened for their ability to grow on degraded alginate. The resultanttransformants were screened for growth on degraded alginate media.Degraded alginate media was prepared by incubating 2% Alginate(Sigma-Aldrich, St. Louis, Mo.) 10 mM Na-Phosphate buffer, 50 mM KCl,400 mM NaCl with alginate lyase from Flavobacterium sp. (Sigma-Aldrich,St. Louis, Mo.) at room temperature for at least one week. This degradedalginate was diluted to a concentration of 0.8% to make growth mediathat had a final concentration of 1×M9 salts, 2 mM MgSO₄, 100 μM CaCl2,0.007% Leucine, 0.01% casamino acids, 1.5% NaCl (this includes allsources of sodium: M9, diluted alginate and added NaCl).

One fosmid-containing E. coli clone was isolated that grew well on thismedia. The fosmid DNA from this clone was isolated and prepared usingFosmidMAX DNA Purification Kit (Epicentre, Madison, Wis.). This isolatedfosmid was transferred back into DH10B cells, and these cells weretested for the ability to grown on alginate.

The results are illustrated in FIG. 4, which shows that certainfosmid-containing E. coli clones are capable of growing on alginate as asole source of carbon. Agrobacterium tumefaciens provides a positivecontrol (see hatched circles). As a negative control, E. coli DH10Bcells are not capable of growing on alginate (see immediate left ofpositive control).

These results also demonstrate that the sequences contained within thisVibrio splendidus derived fosmid clone are sufficient to confer on E.coli the ability to grow on degraded alginate as a sole source ofcarbon. Accordingly, the type II secretion machinery sequences containedwithin the pDONR221 vector (i.e., SEQ ID NO:1), which was harbored bythe original DH10B cells, were not necessary for growth on degradedalginate.

The isolated fosmid sufficient to confer growth alginate as a solesource of carbon was sequenced by Elim Biopharmaceuticals (Hayward,Calif.) using the following primers: UniR3—GGGCGGCCGCAAGGGGTTCGCGTTGGCCGA (SEQ ID NO:147) andPCC1FOS_uni_F—GGAGAAAATACCGCATCAGGCG (SEQ ID NO:148). Sequencing showedthat the vector contained a genomic DNA section that contained the fulllength genes V12B01_(—)24189 to V12B01_(—)24249 (see SEQ ID NOS:2-64).SEQ ID NO:2 shows the nucleotide sequence of entire region betweenV12B01_(—)24189 to V12B01_(—)24249. SEQ ID NOS:3-64 show the individualputative genes contained within SEQ ID NO:2. In this sequence, there isa large gene before V12B01_(—)24189 that is truncated in the fosmidclone. The large gene V12B01_(—)24184 is a putative protein withsimilarity to autotransporters and belongs to COG3210, which is acluster of orthologous proteins that include large exoproteins involvedin heme utilization or adhesion. In the fosmid clone, V12B01_(—)24184 isN-terminally truncated such that the first 5893 bp are missing from thepredicted open reading frame (which is predicted to contain 22889 bp intotal).

Example 2 Engineering E. Coli to Grow on Pectin as a Sole Source ofCarbon

Wild type E. coli is not capable of growing on pectin, di-, ortri-galacturonates as a sole source of carbon. To identify the minimalcomponents to confer on E. coli the capability of growing on pectin, di-and/or tri-galacturonates as a sole source of carbon, an E. coli strainBL21(DE3) harboring both the pBBRGal3P plasmid and the pTrcogl-kdgRplasmid was engineered and tested for the ability to grown on thesepolysaccharides.

The pBBRGal3P plasmid was engineered to contain certain genomic regionof Erwinia carotovora subsp. Atroseptica SCR11043, comprising severalgenes (kdgF, kduI, kduD, pelW, togM, togN, toga, togB, kdgM, and paeX)encoding certain enzymes (kduI, kduD, ogl, pelW and paeX), transporters(togM, togN, togA, togB, and kdgM), and regulatory proteins (kdgR)responsible for the degradation of di- and trigalacturonate. SEQ IDNO:65 shows the nucleotide sequence of the kdgF-PaeX region from Erwiniacarotovora subsp. Atroseptica SCR11043.

To construct this plasmid, the DNA sequence encoding kdgF, kduI, kduD,pelW, togM, togN, togA, togB, kdgM, paeX, ogl, and kdgR of Erwiniacarotovora subsp. Atroseptica SCR11043 was amplified by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 6min, repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-CGGGATCCAAGTTGCAGGATATGACGAAAGCG-3′) (SEQ ID NO:149) and reverse (5′-GCTCTAGAAGATTATCCCTGTCTGCGGAAGCGG-3′) (SEQ ID NO:150) primers, 1 U Phusion HighFidelity DNA polymerase (NEB), and 50 ng Erwinia carotovora subsp.Atroseptica SCR11043 genome (ATCC) in 50 μl.

The vector pBBR1MCS-2 was then amplified by polymerase chain reaction(PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 2.5 min,repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-GCTCTAGAGGGGTGCCTAATGAGTGAGCTAAC-3′) (SEQ ID NO:151) and reverse (5′-CGGGATCCGCGTTAATATTTTGTTAAAATTCGC-3′) (SEQ ID NO:152) primers, 1 U Phusion HighFidelity DNA polymerase (NEB), and 50 ng pBBR1MCS-2 in 50 μl. Bothamplified DNA fragments were digested with BamHI and XbaI and ligated.

The pTrcogl-kdgR plasmid was engineered to contain certain genomicregions of Erwinia carotovora subsp. Atroseptica SCR11043, comprisingtwo genes (ogl and kdgR) encoding an enzyme (ogl) and a regulatoryprotein (kdgR) responsible for degradation of di- and trigalacturonate.SEQ ID NO:66 shows the nucleotide sequence of ogl-kdgR from Erwiniacarotovora subsp. Atroseptica SCR11043.

To prepare this construct, the DNA sequence encoding ogl and kdgR ofErwinia carotovora subsp. Atroseptica SCR11043 was amplified bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 4 min, repeated 30 times. The reaction mixture contained1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward (5′-GCTCTAGAGTTTATGTCGCACCCGCCGTTGG-3′) (SEQ ID NO:153) and reverse (5′-CCCAAGCTTAGAAAGGGAAATTGTGGTAGCCC-3′) (SEQ ID NO:154) primers, 1 U Phusion HighFidelity DNA polymerase (NEB), and 50 ng Erwinia carotovora subsp.Atroseptica SCR11043 genome (ATCC) in 50 μl. The amplified DNA fragmentwas digested with XbaI and HindIII and ligated into pTrc99A pre-digestedwith the same restriction enzymes.

The plasmids pBBRGal3P and pTrcogl-kdgR were co-transformed into E. colistrain BL21(DE3). A single colony was inoculated into LB mediacontaining 50 ug/ml kanamycin and 100 ug/ml ampicillin, and the culturewas grown in incubation shaker with 200 rpm at 37 C. When culturereached OD 600 nm of 0.6, 500 ul of culture was transferred to eppendorftube and centrifuged to pellet the cells. The cells were resuspendedinto 50 ul of M9 media containing 2 mM MgSO₄, 100 uM CaCl₂, 0.4% di- ortrigalacturonate, and 5 ul of this solution was inoculated into 500 ulof fresh M9 media containing 2 mM MgSO₄, 100 uM CaCl₂, 0.4% di- ortrigalacturonate. The culture was grown in incubation shaker with 200rpm at 37 C.

The results in FIG. 5A show that these two plasmids were sufficient toprovide E. coli ability to grow on di- and trigalacturonate as solesource of carbon, but not pectin. In particular, these results show thatthe regions kdgF-paeX and ogl-kdgR were sufficient to confer thisability on E. coli.

Based on the information obtained from the above experiments, it wasconsidered whether the introduction of pectate lyase, pectateacetylesterase, and methylesterase might confer E. coli capability ofgrowing on pectin. To test this hypothesis, E. coli strain DH5αbacterial cells were engineered to contain both the pROU2 plasmid andthe pPEL74 plasmid.

The pROU2 plasmid contains certain genomic regions of Erwiniachrysanthemi, comprising several genes (kdgF, kduI, kduD, pelW, togM,togN, togA, togB, kdgM, paeX, ogl, and kdgR) encoding enzymes (kduI,kduD, ogl, pelW, and paeX), transporters (togM, togN, togA, togB, andkdgM), and regulatory proteins (kdgR) responsible for degradation of di-and trigalacturonate.

The pPEL74 plasmid contains certain genomic regions of Erwiniachrysanthemi, comprising several genes (pelA, pelE, paeY, and pem)encoding pectate lyases (pelA and pelE), pectin acetylesterases (paeY),and pectin methylesterase (pem).

As shown in FIG. 5B, E. coli DH5a engineered with pROU2 and pPEL74 wasable to grow on pectin as a sole source of carbon, showing that thegenes contained within these plasmids are sufficient to confer thisproperty on an organism that is otherwise incapable of growing on pectinas a sole source of carbon.

Example 3 In Vitro Conversion of Alginate to Pyruvate andGlyceraldehyde-3-Phosphate

The ability of an enzyme mixture containing all required enzymes foralginate degradation and metabolism was investigated for its ability toproduce pyruvate from alginate. In addition, various novel alcoholdehydrogenases (ADHs), such as ADH1-12 (see SEQ ID NOS:69-92), isolatedfrom Agrobacterium tumefaciens, were tested for their ability tocatalyze either DEHU or mannuronate hydrogenation.

A simplified metabolic pathway for alginate degradation and metabolismis shown in FIG. 2. Alginate can be degraded by at least two differentmethodologies: enzymatic and chemical methodologies.

In enzymatic degradation, the degradation of alginate is catalyzed by afamily of enzymes called alginate lyases. For this experiment, Atu3025was used. Atu3025 is an exolytically acting enzyme and yields DEHU fromalginate polymer. DEHU is converted to the common hexuronate metabolite,KDG. This reaction is catalyzed by alcohol dehydrogenases (e.g., DEHUhydrogenases).

Chemical degradation catalyzed by acid solution, such as formate, yieldsa monosaccharide mannuronate. Mannuronate is then converted tomannonate, which is catalyzed by enzymes with mannonate dehydrogenase(mannuronate reductase) activity. In bacteria, mannonate dehydratase(UxuA) catalyzes dehydration from mannuronate to form KDG.

KDG is readily metabolized to form of pyruvate andglyceraldehydes-3-phosphate (G3P). KDG is first phosphorylated toKDG-6-phosphate (KDGP), which is catalyzed by KDG kinase, and thenbroken down to pyruvate and G3P, which is catalyzed by KDGP aldolase.

Preparation of oligoalginate lyase Atu3025 derived from Agrobacteriumtumefaciens C58. pETAtu3025 was constructed based on pET29 plasmidbackbone (Novagen). The oligoalginate lyase Atu3025 was amplified byPCR: 98° C. for 10 sec, 55° C. for 15 sec, and 72° C. for 60 sec,repeated for 30 times. The reaction mixture contained 1× Phusion buffer,2 mM dNTP, 0.5 μM forward (5′-GGAATTCCATATGCGTCCCTCTGCCCCGGCC-3′) (SEQID NO:155) and reverse (5′-CGGGATCCTTAGAACTGCTTGGGAAGGGAG-3′) (SEQ IDNO:156) primers, 2.5 U Phusion DNA polymerase (Finezyme), and an aliquotof Agrobacterium tumefaciens C58 (gift from Professor Eugene Nester,University of Washington) cells as a template in total volume of 100 μl.The amplified fragment was digested with NdeI and BamHI and ligated intopET29 pre-digested with the same enzymes using T4 DNA ligase to formpETAtu3025. The constructed plasmid was sequenced (ElimBiopharmaceuticals) and the DNA sequence of the insert was confirmed.The nucleotide sequence of the Atu3025 insert is provided in SEQ IDNO:67. The polypeptide sequence encoded by the Atu3025 insert isprovided in SEQ ID NO:68.

The pETAtu3025 was transformed into Escherichia coli strain BL21(DE3). Acolony of BL21(DE3) containing pETAtu3025 was inoculated into 50 ml ofLB media containing 50 μg/ml kanamycin (Km⁵⁰). This strain was grown inan orbital shaker with 200 rpm at 37° C. The 0.2 mM IPTG was added tothe culture when the OD_(600 nm) reached 0.6, and the induced culturewas grown in an orbital shaker with 200 rpm at 20° C. 24 hours after theinduction, the cells were harvested by centrifugation at 4,000 rpm×g for10 min and the pellet was resuspended into 2 ml of Bugbuster (Novagen)containing 10 μl of Lysonase™ Bioprocessing Reagent (Novagen). Thesolution was again centrifuged at 4,000 rpm×g for 10 min and thesupernatant was obtained.

Construction of pETADH1 through pETADH12. DNA sequences of ADH1-12 ofAgrobacterium tumefaciens C58 were amplified by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1min, repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (Table 1) and reverse (Table 1)primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngAgrobacterium tumefaciens C58 genome in 50 μl. Amplified DNA fragmentwas digested with NdeI and BamHI and ligated into pET28 pre-digestedwith the same restriction enzymes. For DNA sequences with internal NdeIor BamHI site, front and bottom half sequences of each ADH were firstamplified using described method. The resulting two DNA fragments weregel purified and spliced by overlapping PCR.

TABLE 1Primers used to amplify ADH1-12 from Agrobacterium tumefaciens C58. A.tumefaciens Name C58 Forward Primer Reverse Primer ADH1 Atu1557GGAATTCCATATGTTCACAACGTCCGCCTA GCTTGACGGCCATGTGGCCGAGGCCGC(SEQ ID NO: 276) (SEQ ID NO: 277) GCGGCCTCGGCCACATGGCCGTCAAGCCGGGATCCTTAGGCGGCCTTCTGGCGCG (SEQ ID NO: 278) (SEQ ID NO: 279) ADH2Atu2022 GGAATTCCATATGGCTATTGCAAGAGGTTA CGGGATCCTTAAGCGTCGAGCGAGGCCA(SEQ ID NO: 280) (SEQ ID NO: 281) ADH3 Atu0626GGAATTCCATATGACTAAAACAATGAAGGC CACCGGGGCCGGGGTCCGGTATTGCCA(SEQ ID NO: 282) (SEQ ID NO: 283) TGGCAATACCGGACCCCGGCCCCGGTGCGGGATCCTTAGGCGGCGAGATCCACGA (SEQ ID NO: 284) (SEQ ID NO: 285) ADH4Atu5240 GGAATTCCATATGACCGGGGCGAACCAGCC ATAGCCGCTCATACGCCTCGGTTGCCT(SEQ ID NO: 286) (SEQ ID NO: 287) AGGCAACCGAGGCGTATGAGCGGCTATCGGGATCCTTAAGCGCCGTGCGGAAGGA (SEQ ID NO: 288) (SEQ ID NO: 289) ADH5Atu3163 GGAATTCCATATGACCATGCATGCCATTCA CGGGATCCTTATTCGGCTGCAAATTGCA(SEQ ID NO: 290) (SEQ ID NO: 291) ADH6 Atu2151GGAATTCCATATGCGCGCGCTTTATTACGA CGGGATCCTTATTCGAACCGGTCGATGA(SEQ ID NO: 292) (SEQ ID NO: 293) ADH7 Atu2814GGAATTCCATATGCTGGCGATTTTCTGTGA CGGGATCCTTATGCGACCTCCACCATGC(SEQ ID NO: 294) (SEQ ID NO: 295) ADH8 Atu5447GGAATTCCATATGAAAGCCTTCGTCGTCGA CGGGATCCTTAGGATGCGTATGTAACCA(SEQ ID NO: 296) (SEQ ID NO: 297) ADH9 Atu4087GGAATTCCATATGAAAGCGATTGTCGCCCA CGGGATCCTTAGGAAAAGGCGATCTGCA(SEQ ID NO: 298) (SEQ ID NO: 299) ADH10 Atu4289GGAATTCCATATGCCGATGGCGCTCGGGCA CGGGATCCTTAGAATTCGATGACTTGCC(SEQ ID NO: 300) (SEQ ID NO: 301) ADH11 Atu3027GGAATTCCATATGAAACATTCTCAGGACAA GGGCGCCGATCATGTGGTGCGTTTCCG(SEQ ID NO: 302) (SEQ ID NO: 303) CGGAAACGCACCACATGATCGGCGCCCCGGGATCCTTATGCCATACGTTCCATAT (SEQ ID NO: 304) (SEQ ID NO: 305) ADH12 Atu3026 GGAATTCCATATGCAGCGTTTTACCAACAG CGGGATCCTTAGGAAAACAGGACGCCGC(SEQ ID NO: 306) (SEQ ID NO: 307)

Expression and Purification of ADH 1-10.

All plasmids were transformed into Escherichia coli strain BL21(DE3).The single colonies of BL21(DE3) containing respective alcoholdehydrogenase (ADH) genes were inoculated into 50 ml of LB mediacontaining 50 μg/ml kanamycin (Km⁵⁰). These strains were grown in anorbital shaker with 200 rpm at 37° C. The 0.2 mM IPTG was added to eachculture when the OD_(600 nm) reached 0.6, and the induced culture wasgrown in an orbital shaker with 200 rpm at 20° C. 24 hours after theinduction, the cells were harvested by centrifugation at 4,000 rpm×g for10 min and the pellet was resuspended into 2 ml of Bugbuster (Novagen)containing 10 μl of Lysonase™ Bioprocessing Reagent (Novagen). Thesolution was again centrifuged at 4,000 rpm×g for 10 min and thesupernatant was obtained.

Preparation of ˜2% DEHU Solution by Enzymatic Degradation.

DEHU solution was enzymatically prepared. A 2% alginate solution wasprepared by adding 10 g of low viscosity alginate into the 500 ml of 20mM Tris-HCl (pH7.5) solution. An approximately 10 mg of alginate lyasederived from Flavobacterium sp. (purchased from Sigma-aldrich) was addedto the alginate solution. 250 ml of this solution was then transferredto another bottle and the E. coli cell lysate containing Atu3025prepared above section was added. The alginate degradation was carriedout at room temperature over night. The resulting products were analyzedby thin layer chromatography, and DEHU formation was confirmed.

Preparation of D-Mannuronate Solution by Chemical Degradation.

D-mannuronate solution was chemically prepared based on the protocolpreviously described by Spoehr (Archive of Biochemistry, 14: pp153-155). Fifty milligram of alginate was dissolved into 800 μL ofninety percent formate. This solution was incubated at 100° C. for overnight. Formate was then evaporated and the residual substances werewashed with absolute ethanol twice. The residual substance was againdissolved into absolute ethanol and filtrated. Ethanol was evaporatedand residual substances were resuspended into 20 mL of 20 mM Tris-HCl(pH 8.0) and the solution was filtrated to make a D-mannuronatesolution. This D-mannuronate solution was diluted 5-fold and used forassay.

Assay for DEHU Hydrogenase.

To identify DEHU hydrogenase, a NADPH dependent DEHU hydrogenation assaywas performed. 20 μl of prepared cell lysate containing each ADH wasadded to 160 μl of 20-fold deluted DEHU solution prepared in the abovesection. 20 μl of 2.5 mg/ml of NADPH solution (20 mM Tris-HCl, pH 8.0)was added to initiate the hydrogenation reaction, as a preliminary studyusing cell lysate of A. tumefaciens C58 have shown that DEHUhydrogenation requires NADPH as a co-factor. The consumption of NADPHwas monitored an absorbance at 340 nm for 30 min using the kinetic modeof ThermoMAX 96 well plate reader (Molecular Devises). E. coli celllysate containing alcohol dehydrogenase (ADH) 10 lacking a portion ofN-terminal domain was used in a control reaction mixture.

Assay for D-Mannuronate Hydrogenase.

To identify D-mannuronate hydrogenase, a NADPH dependent D-mannuronatehydrogenation assay was performed. 20 μl of prepared cell lysatecontaining each ADH was added to 160 μl of D-mannuronate solutionprepared in the above section. 20 μl of 2.5 mg/ml of NADPH solution (20mM Tris-HCl, pH 8.0) was added to initiate the hydrogenation reaction.The consumption of NADPH was monitored an absorbance at 340 nm for 30min using the kinetic mode of ThermoMAX 96 well plate reader (MolecularDevises). E. coli cell lysate containing alcohol dehydrogenase (ADH) 10lacking a portion of N-terminal domain was used in a control reactionmixture.

Construction of pETkdgK.

DNA sequence of kdgK of Escherichia coli encoding 2-keto-deoxy gluconatekinase was amplified by polymerase chain reaction (PCR): 98° C. for 10sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-AGGTACGGTGAAATAA AGGAGG ATATACAT ATGTCCAAAAAGATTGCCGT-3′)(SEQ ID NO:157) and reverse(5′-TTTTCCTTTTGCGGCCGCCCCGCTGGCATCGCCTCAC-3′) (SEQ ID NO:158) primers, 1U Phusion High Fidelity DNA polymerase (NEB), and 50 ng Escherichia coliDH10B genome in 50 μl. Amplified DNA fragment was digested with NdeI andNotI and ligated into pET29 pre-digested with the same restrictionenzymes.

Construction of pETkd2A.

DNA sequence of kdgA Escherichi coli encoding 2-keto-deoxygluconate-6-phosphate aldolase was amplified by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1min, repeated 30 times. The reaction mixture contained 1×Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-GGCGATGCCAGCGTAA AGGAGG ATATACATATGAAAAACTGGAAAACAAG-3′) (SEQ ID NO:159) and reverse(5′-TTTTCCTTTTGCGGCCGCCCCAGCTTAGCGCCTTCTA-3′) (SEQ ID NO:160) primers, 1U Phusion High Fidelity DNA polymerase (NEB), and 50 ng Escherichia coliDH10B genome in 50 μl. Amplified DNA fragment was digested with NdeI andNotI and ligated into pET29 pre-digested with the same restrictionenzymes.

Protein Expression and Purification.

All plasmids (pETAtu3025, pETADH11, pETADH12, pETkdgA, pETkdgK, andpETuxuA) were transformed into Escherichia coli strain BL21(DE3). Thesingle colonies of BL21(DE3) containing respective plasmids wereinoculated into 50 ml of LB media containing 50 μg/ml kanamycin (KM⁵⁰).These strains were grown in an orbital shaker with 200 rpm at 37° C. The0.2 mM IPTG was added to each culture when the OD_(600 nm) reached 0.6,and the induced culture was grown in an orbital shaker with 200 rpm at20° C. 24 hours after the induction, the cells were harvested bycentrifugation at 4,000 rpm×g for 10 min and the pellet was resuspendedinto 2 ml of Bugbuster (Novagen) containing 10 μl of Lysonase™Bioprocessing Reagent (Novagen) and suggested amount of proteaseinhibitor cocktail (SIGMA). The solution was again centrifuged at 4,000rpm×g for 10 min and the supernatant was obtained. The supernatant wasapplied to Nickel-NTA spin column (Qiagen) to purify His-taggedproteins.

The results of the assays for DEHU hydrogenase activity andD-mannuronate hydrogenase activity of ADH1-10 are shown in FIGS. 7A and7B. These results demonstrate that the novel enzymes ADH1 and ADH2showed significant DEHU hydrogenase activity (FIG. 7A), and that thenovel enzymes ADH3, ADH4, and ADH9 showed significant mannuronatehydrogenase activity (FIG. 7B).

In Vitro Pyruvate Formation.

The reaction mixture contained 1% alginate or ˜0.5% mannuronate, ˜5 ugof purified Atu3026 (ADH12) or Atu3027 (ADH11), and ˜5 ug of purifiedoligoalginate lyase (Atu3025), UxuA, KdgK, and KdgA, 2 mM of ATP, and0.6 mM of NADPH in 20 mM Tris-HCl pH7.0. The reaction was carried outover night and the pyruvate formation was monitored by the pyruvateassay kit (BioVision, Inc).

The results of in vitro pyruvate formation from alginate mediated byenzymatic and chemical degradation are shown in FIG. 6B and FIG. 6C,respectively. As can be seen in these figures, alginate was converted topyruvate via the isolated enzymes. These results also show that each ofAtu3026 (ADH12) and Atu3027 (ADH11) are capable of catalyzing both DEHUhydrogenase and mannuronate hydrogenase reactions.

Example 4 Construction and Biological Activity of Biosynthesis PathwaysConstruction of Pathways:

A propionaldehyde biosynthetic pathway comprising a threonine deaminase(ilvA) gene from Escherichia coli and keto-isovalerate decarboxylase(kivd) from Lactococcus lactis is constructed and tested for the abilityto convert L-threonine to propionaldehyde.

A butyraldehyde biosynthetic pathway comprising a thiolase (atoB) genefrom E. coli, β-hydroxy butyryl-CoA dehydrogenase (hbd), crotonase(crt), butyryl-CoA dehydrogenase (bcd), electron transfer flavoprotein A(etfA), and electron transfer flavoprotein B (etfB)genes fromClostridium acetobutyricum ATCC 824, and a coenzyme A-linkedbutyraldehyde dehydrogenase (ald) gene from Clostridium beijerinckiiacetobutyricum ATCC 824 was constructed in E. coli and tested for theability to produce butyraldehyde. Also, a coenzyme A-linked alcoholdehydrogenase (adhE2) gene from Clostridium acetobutyricum ATCC 824 wasused as an alternative to ald and tested for the ability to producebutanol.

An isobutyraldehyde biosynthetic pathway comprising an acetolactatesynthase (alsS) from Bacillus subtilis or (als) from Klebsiellapneumoniae subsp. pneumoniae MGH 78578 (codon usage was optimized for E.coli protein expression) and acetolactate reductoisomerase (ilvC) and2,3-dihydroxyisovalerate dehydratase (ilvD), genes from E. coli andketo-isovalerate decarboxylase (kivd) from Lactococcus lactis wasconstructed and tested for the ability to produce isobutyraldehyde, asmeasured by isobutanal production.

3-methylbutyraldehyde and 2-methylbutyraldehyde biosynthesis pathwayscomprising an acetolactate synthase (alsS) from Bacillus subtilis or(als) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (codonusage was optimized for E. coli protein expression), acetolactatereductoisomerase (ilvC), 2,3-dihydroxyisovalerate dehydratase (ilvD),isopropylmalate synthase (LeuA), isopropylmalate isomerase (LeuC andLeuD), and 3-isopropylmalate dehydrogenase (LeuB) genes from E. coli andketo-isovalerate decarboxylase (kivd) from Lactococcus lactis wereconstructed and tested for the ability to produce 3-isovaleraldehyde and2-isovaleraldehyde.

Phenylacetoaldehyde and 4-hydroxyphenylacetoaldehyde biosynthesispathways comprising a transketolase (tktA), a3-deoxy-7-phosphoheptulonate synthase (aroF, aroG, and aroH),3-dehydroquinate synthase (aroB), a 3-dehydroquinate dehydratase (aroD),a dehydroshikimate reductase (aroE), a shikimate kinase II (aroL), ashikimate kinase I (aroK), a 5-enolpyruvylshikimate-3-phosphatesynthetase (aroA), a chorismate synthase (aroC), a fused chorismatemutase P/prephenate dehydratase (pheA), and a fused chorismate mutaseT/prephenate dehydrogenase (tyrA) genes from E. coli, keto-isovaleratedecarboxylase (kivd) from Lactococcus lactis were constructed and testedfor the ability to produce phenylacetoaldehyde and/or4-hydroxyphenylacetoaldehyde.

A 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and 2-(indole-3-)ethanolbiosynthesis pathway comprising a transketolase (tktA), a3-deoxy-7-phosphoheptulonate synthase (aroF, aroG, and aroH),3-dehydroquinate synthase (aroB), a 3-dehydroquinate dehydratase (aroD),a dehydroshikimate reductase (aroE), a shikimate kinase II (aroL), ashikimate kinase I (aroK), a 5-enolpyruvylshikimate-3-phosphatesynthetase (aroA), a chorismate synthase (aroC), a fused chorismatemutase P/prephenate dehydratase (pheA), and a fused chorismate mutaseT/prephenate dehydrogenase (tyrA) genes from E. coli, keto-isovaleratedecarboxylase (kivd) from Lactococcus lactis, alcohol dehydrogenase(adh2) from Saccharomyces cerevisiae, Indole-3-pyruvate decarboxylase(ipdc) from Azospirillum brasilense, phenylethanol reductase (par) fromRhodococcus sp. ST-10, and benzaldehyde lyase (bal) from Pseudomonasfluorescence was constructed and tested for the ability to produce2-phenylethanol, 2-(4-hydroxyphenyl)ethanol and/or 2-(indole-3)ethanol.

Construction of pBADButP.

The DNA sequence encoding hbd, crt, bcd, etfA, and etfB of Clostridiumacetobutyricum ATCC 824 was amplified by polymerase chain reaction(PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 3 min,repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-CCCGAGCTCTTAGGAGGATTAGTCATGGAAC-3′)(SEQ ID NO:161) and reverse (5′-GCTCTAGA TTATTTTGAATAATCGTAGAAACC-3′)(SEQ ID NO:162) primers, 1 U Phusion High Fidelity DNA polymerase (NEB),and 50 ng Clostridium acetobutyricum ATCC 824 genome (ATCC) in 50 μl.Amplified DNA fragment was digested with BamHI and XbaI and ligated intopBAD33 pre-digested with the same restriction enzymes.

Construction of pBADButP-atoB.

The DNA sequence encoding atoB of Escherichia coli DH10B was amplifiedby polymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15sec, and 72° C. for 1 min, repeated 30 times. The reaction mixturecontained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-GCTCTAGAGGAGGATATATATATGAAAAATTGTGTCATCGTC-3′) (SEQ ID NO:163) andreverse (5′-AA CTGCAGTTAATTCAACCGTTCAATCACC-3′) (SEQ ID NO:164) primers,1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ng Escherichiacoli DH10B genome in 50 μl. Amplified DNA fragment was digested withXbaI and PstI and ligated into pBADButP pre-digested with the samerestriction enzymes.

Construction of pBADatoB-ald.

The DNA sequence encoding atoB of Escherichia coli DH10B and ald fromClostridium beijerinckii were amplified separately by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1min, repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-CGAGCTCAGGAGGATATATATATGAAAAATTGTGTCATCGTCAGTG-3′) (SEQ ID NO:165) for atoB and5′-GGTTGAATTAAGGAGGATATATATATGAATAAAGACACACTAATACCTAC-3′ for ald) (SEQID NO:166) and reverse(5′-GTCTTTATTCATATATATATCCTCCTTAATTCAACCGTTCAATCACCATC-3′ (SEQ IDNO:146) for atoB and 5′-CCCAAGCTTAGCCGGCAAGTACACATCTTC-3′ for ald) (SEQID NO:167) primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and50 ng Escherichia coli DH10B and Clostridium beijerinckii genome (ATCC)in 501, respectively. The amplified DNA fragments were gel purified andeluted into 30 ul of EB buffer (Qiagen). 5 ul from each DNA solution wascombined and each DNA fragment was spliced by another round of PCR: 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 2 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward (5′-CGAGCTCAGGAGGATATATATATGAAAAATTGTGTCATCGTCAGTG-3′) (SEQ ID NO:168) and reverse(5′-CCCAAGCTTAGCCGGCAAGTACACATCTTC-3′) (SEQ ID NO:169) primers, 1 UPhusion High Fidelity DNA polymerase (NEB). The spliced fragment wasdigested with SacI and HindIII and ligated into pBADButP pre-digestedwith the same restriction enzymes.

Construction of pBADButP-atoB-ALD.

The DNA fragment 1 encoding chloramphenicol acetyltransferase (CAT), P15origin of replication, araBAD promoter, atoB of Escherichia coli DH10Band ald of Clostridium beijerinckii and the DNA fragment 2 encodingaraBAD promoter, hbd, crt, bcd, etfA, and etfB of Clostridiumacetobutyricum ATCC 824 were amplified separately by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 4min, repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward(5′-AAGGAAAAAAGCGGCCGCCCCTGAACCGACGACCGGGTCG-3′) (SEQ ID NO:170) forfragment 1 and 5′-CGGGGTACCACTTTTCATACTCCCGCCATTCAG-3′ (SEQ ID NO:274)for fragment 2, and reverse (5′-CGGGGTACCGCGGATACATATTTGAATGTATTTAG-3′)(SEQ ID NO:171) for fragment 1 and(5′-AAGGAAAAAAGCGGCCGCGCGGATACATATTTGAATGTATTTAG-3′) (SEQ ID NO:172) forfragment 2) primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and50 ng pBADatoB-ald and pBADButP in 50 μl, respectively. Amplified DNAfragments were digested with NotI and KpnI and ligated each other.

Construction of pBADilvCD.

The DNA fragments encoding ilvC and ilvD of Escherichia coli DH10B wereamplified separately by polymerase chain reaction (PCR): 98° C. for 10sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-GCTCTAGAGGAGGATATATATATGGCTAACTACTTCAATACAC-3′) (SEQ IDNO:173) for ilvC and5′-TGCTGTTGCGGGTTAAGGAGGATATATATATGCCTAAGTACCGTTCCGCC-3′ for ilvD) (SEQID NO:174) and reverse(5′-AACGGTACTTAGGCATATATATATCCTCCTTAACCCGCAACAGCAATACG-3′) (SEQ IDNO:175) for ilvC and 5′-ACATGCATGCTTAACCCCCCAGTTTCGATT-3′) (SEQ IDNO:176) for ilvD) primers, 1 U Phusion High Fidelity DNA polymerase(NEB), and 50 ng Escherichia coli DH10B genome (ATCC) in 50 μl. Theamplified DNA fragments were gel purified and eluted into 30 ul of EBbuffer (Qiagen). 5 ul from each DNA solution was combined and each DNAfragment was spliced by another round of PCR: 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 2 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-GCTCTAGAGGAGGATATATATATGGCTAACTACTTCAATACAC-3′) (SEQ ID NO:177) andreverse (5′-ACATGCATGCTTAACCCCCCAGTTTCGATT-3′) (SEQ ID NO:178) primers,1 U Phusion High Fidelity DNA polymerase (NEB). The spliced fragment wasdigested with XbaI and SphI and ligated into pBAD33 pre-digested withthe same restriction enzymes.

Construction of pBADals-ilvCD.

The DNA fragment encoding als of Klebsiella pneumoniae subsp. pneumoniaeMGH 78578 of its codon usage optimized for over-expression in E. coliwas amplified by polymerase chain reaction (PCR): 98° C. for 10 sec, 60°C. for 15 sec, and 72° C. for 1 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGGATAAACAGTATCCGGT-3′) (SEQ ID NO:179) andreverse (5′-GCTCTAGATTACAGAATTTGACTCAGGT-3′) (SEQ ID NO:180) primers, 1U Phusion High Fidelity DNA polymerase (NEB), and 50 ng pETals in 50 μl.The amplified DNA fragment was digested with SacI and XbaI and ligatedinto pBADilvCD pre-digested with the same restriction enzymes.

Construction of pBADalsS-ilvCD.

The DNA fragments encoding front and bottom halves of alsS of Bacillussubtilis B26 were amplified by polymerase chain reaction (PCR): 98° C.for 10 sec, 60° C. for 15 sec, and 72° C. for 0.5 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGTTGACAAAAGCAACAAAAG-3′) (SEQ ID NO:181)for front and 5′-CGGTACCCTTTCCAGAGATTTAGAG-3′ (SEQ ID NO:275) for backhalves, and reverse (5′-CTCTAAATCTCTGGAAAGGGTACCG-3′) (SEQ ID NO:182)for front and (5′-GCTCTAGATTAGAGAGCTTTCGTTTTCATG-3′ for back halves)(SEQ ID NO:183) primers, 1 U Phusion High Fidelity DNA polymerase (NEB),and 50 ng Bacillus subtilis B26 genome (ATCC) in 50 μl. The amplifiedDNA fragments were gel purified and eluted into 30 ul of EB buffer(Qiagen). 5 ul from each DNA solution was combined and each DNA fragmentwas spliced by another round of PCR: 98° C. for 10 sec, 60° C. for 15sec, and 72° C. for 1 min, repeated 30 times. The reaction mixturecontained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGTTGACAAAAGCAACAAAAG-3′) (SEQ ID NO:184)and reverse (5′-GCTCTAGATTAGAGAGCTTTCGTTTTCATG-3′) (SEQ ID NO:185)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was internal XbaI site free and thus was digested with SacI andXbaI and ligated into pBADilvCD pre-digested with the same restrictionenzymes.

Construction of pBADLeuABCD.

The DNA fragment encoding leuA, leuB, leuC, and leuD of Escherichia coliBL21(DE3) was amplified by polymerase chain reaction (PCR): 98° C. for10 sec, 60° C. for 15 sec, and 72° C. for 3 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CGAGCTCAGGAGGATATATATATGAGCCAGCAAGTCATTATTTTCG-3′) (SEQ IDNO:186) and reverse (5′-AAAACTGCAGCGTTTGATGACGTGGACGATAGCGG-3′) (SEQ IDNO:187) primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50ng Escherichia coli BL21(DE3) genome in 50 μl. The amplified DNAfragment was digested with SacI and XbaI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADLeuABCD2.

The DNA fragment 1 encoding leuA and leuB and the DNA fragment 2encoding leuC and leuD of Escherichia coli BL21 (DE3) were amplified bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 1 min, repeated 30 times. The reaction mixture contained1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CGAGCTCAGGAGGATATATATATGAGCCAGCAAGTCATTATTTTCG-3′) (SEQ ID NO:188)for fragment 1 and(5′-AGGGGTGTAAGGAGGATATATATATGGCTAAGACGTTATACGAAAAATTG-3′) (SEQ IDNO:189) for fragment 2 and reverse(5′-CGTCTTAGCCATATATATATCCTCCTTACACCCCTTCTGCTACATAGCGG-3′) (SEQ IDNO:190) for fragment 1 and (5′-AAAACTGCAGCGTTTGATGACGTGGACGATAGCGG-3′)(SEQ ID NO:191) for fragment 2 primers, 1 U Phusion High Fidelity DNApolymerase (NEB), and 50 ng Escherichia coli BL21(DE3) genome in 50 μl,respectively. The amplified DNA fragments were gel purified and elutedinto 30 ul of EB buffer (Qiagen). 5 ul from each DNA solution wascombined and each DNA fragment was spliced by another round of PCR: 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 3 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CGAGCTCAGGAGGATATATATATGAGCCAGCAAGTCATTATTTTCG-3′) (SEQ ID NO:192)and reverse (5′-AAAACTGCAGCGTTTGATGACGTGGACGATAGCGG-3′) (SEQ ID NO:193)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and XbaI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADLeuABCD4.

The DNA fragments encoding leuA, leuB, leuC and leuD of Escherichia coliBL21(DE3) were amplified by polymerase chain reaction (PCR): 98° C. for10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CGAGCTCAGGAGGATATATATATGAGCCAGCAAGTCATTATTTTCG-3′) (SEQ IDNO:194) for leuA,(5′-GAAACCGTGTGAGGAGGATATATATATGTCGAAGAATTACCATATTGCCG-3′) (SEQ IDNO:195) for leuB,(5′-AGGGGTGTAAGGAGGATATATATATGGCTAAGACGTTATACGAAAAATTG-3′) (SEQ IDNO:196) for leuC, and(5′-ACATTAAATAAGGAGGATATATATATGGCAGAGAAATTTATCAAACACAC-3′) (SEQ IDNO:197) for leuD and reverse(5′-ATTCTTCGACATATATATATCCTCCTCACACGGTTTCCTTGTTGTTTTCG-3′) (SEQ IDNO:198) for leuA,(5′-CGTCTTAGCCATATATATATCCTCCTTACACCCCTTCTGCTACATAGCGG-3′) (SEQ IDNO:199) for leuB,(5′-TTTCTCTGCCATATATATATCCTCCTTATTTAATGTTGCGAATGTCGGCG-3′) (SEQ IDNO:200) for leuC, and (5′-AAAACTGCAGCGTTTGATGACGTGGACGATAGCGG-3′) (SEQID NO:201) for leuD primers, 1 U Phusion High Fidelity DNA polymerase(NEB), and 50 ng Escherichia coli BL21(DE3) genome in 50 μl,respectively. The amplified DNA fragments were gel purified and elutedinto 30 ul of EB buffer (Qiagen). 5 ul from each DNA solution wascombined and each DNA fragment was spliced by another round of PCR: 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 3 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CGAGCTCAGGAGGATATATATATGAGCCAGCAAGTCATTATTTTCG-3′) (SEQ ID NO:202)and reverse (5′-AAAACTGCAGCGTTTGATGACGTGGACGATAGCGG-3′) (SEQ ID NO:203)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and XbaI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADals-ilvCD-leuABCD, pBADals-ilvCD-leuABCD2pBADals-ilvCD-leuABCD4 pBADalsS-ilvCD-leuABCD, pBADalsS-ilvCD-leuABCD2pBADalsS-ilvCD-leuABCD4.

The DNA fragments 1 (for als) and 2 (for alsS) encoding chloramphenicolacetyltransferase (CAT), P15 origin of replication, araBAD promoter, alsof Klebsiella pneumoniae subsp. pneumoniae MGH 78578 of its codon usageoptimized for over-expression in E. coli or alsS of Bacillus subtilisB26 and ilvC and ilvD of E. coli DH 10B were amplified separately bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 4 min, repeated 30 times. The reaction mixture contained1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-AAGGAAAAAAGCGGCCGCCCCTGAACCGACGACCGGGTCG-3′) (SEQ ID NO:204) andreverse (5′-CGGGGTACCGCGGATACATATTTGAATGTATTTAG-3′) (SEQ ID NO:205)primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngpBADals-ilvCD and pBADalsS-ilvCD in 50 μl, respectively.

To remove an internal SphI restriction enzyme site form leuC, overlapPCR was carried out. The front and bottom halves of DNA fragment 3 (forleuABCD), fragment 4 (for leuABCD2), and fragment 5 (for leuABCD4)encoding araBAD promoter, leuA, leuB, leuC, and leuD of E. coliBL21(DE3) were amplified separately by polymerase chain reaction (PCR):98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 4 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward (5′-AAGGAAAAAAGCGGCCGCACTTTTCATACTCCCGCCATTCAG-3′)(SEQ ID NO:206) for front and (5′-CAAAGGCCGTCTGCACGCGCCGAAAGGCAAA-3′)(SEQ ID NO:207) for back halves) and reverse(5′-TTTGCCTTTCGGCGCGTGCAGACGGCCTTTG-3′) (SEQ ID NO:208) for front and(5′-ACATGCATGCCGTTTGATGACGTGGACGATAGCGG-3′) (SEQ ID NO:209) for bottomhalves, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngpBADleuABCD, pBADleuABCD2, and pBADleuABCD4 in 50 μl, respectively. Theamplified DNA fragments were gel purified and eluted into 30 ul of EBbuffer (Qiagen). 5 ul from each DNA solution was combined and each DNAfragment was spliced by another round of PCR: 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 4 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-AAGGAAAAAAGCGGCCGCACTTTTCATACTCCCGCCATTCAG-3′) (SEQ ID NO:210) andreverse (5′-ACATGCATGCCGTTTGATGACGTGGACGATAGCGG-3′) (SEQ ID NO:211)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The resultingfragment 3, 4, and 5 were digested with SphI and NotI and ligated intoboth fragment 1 and 2 pre-digested with the same restriction enzymes.

Construction of pBADaroG-tktA-aroBDE.

The DNA fragments encoding aroG, tktA, aroB, aroD, and aroE ofEscherichia coli BL21(DE3) were amplified by polymerase chain reaction(PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1 min,repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-CCCGAGCTCAGGAGGATATATATATGAATTATCAGAACGACGATTTAC-3′) (SEQ ID NO:212) for aroG,(5′-GCGTCGCGGGTAAGGAGGAAAATTTTATGTCCTCACGTAAAGAGCTTGCC-3′) (SEQ IDNO:213) for tktA,(5′-GAACTGCTGTAAGGAGGTTAAAATTATGGAGAGGATTGTCGTTACTCTCG-3′) (SEQ IDNO:214) foraroB,}(5′-CAATCAGCGTAAGGAGGTATATATAATGAAAACCGTAACTGTAAAAGATC-3′) (SEQ IDNO:215) for aroD, and(5′-TACACCAGGCATAAGGAGGAATTAATTATGGAAACCTATGCTGTTTTTGG-3′) (SEQ IDNO:216) for aroE and reverse(5′-TACGTGAGGACATAAAATTTTCCTCCTTACCCGCGACGCGCTTTTACTGC-3′) (SEQ IDNO:217) for aroG,(5′-CAATCCTCTCCATAATTTTAACCTCCTTACAGCAGTTCTTTTGCTTTCGC-3′) (SEQ IDNO:218) for tktA,(5′-CAATCAGCGTAAGGAGGTATATATAATGAAAACCGTAACTGTAAAAGATC-3′) (SEQ IDNO:219) for aroB,(5′-TACGGTTTTCATTATATATACCTCCTTACGCTGATTGACAATCGGCAATG-3′) (SEQ IDNO:220) for aroD, and (5′-ACATGCATGCTTACGCGGACAATTCCTCCTGCAA-3′) (SEQ IDNO:221) for aroE, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50ng Escherichia coli BL21(DE3) genome in 50 μl, respectively. Theamplified DNA fragments were gel purified and eluted into 30 ul of EBbuffer (Qiagen). 5 ul from each DNA solution was combined and each DNAfragment was spliced by another round of PCR: 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 3 min, repeated 30 times. The reactionmixture contained 1×Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGAATTATCAGAACGACGATTTAC-3′) (SEQ ID NO:222)and reverse (5′-ACATGCATGCTTACGCGGACAATTCCTCCTGCAA-3′) (SEQ ID NO:223)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and SphI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADpheA-aroLAC.

The DNA fragments encoding pheA, aroL, aroA, and aroC of Escherichiacoli DH10 were amplified by polymerase chain reaction (PCR): 98° C. for10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CCCGAGCTCAGGAGGATATATATATGACATCGGAAAACCCGTTACTGG-3′) (SEQ IDNO:224) for pheA,(5′-GATCCAACCTAAGGAGGAAAATTTTATGACACAACCTCTTTTTCTGATCG-3′) (SEQ IDNO:225) for aroL,(5′-GATCAATTGTTAAGGAGGTATATATAATGGAATCCCTGACGTTACAACCC-3′) (SEQ IDNO:226) for aroA, and(5′-CAGGCAGCCTAAGGAGGAATTAATTATGGCTGGAAACACAATTGGACAAC-3′) (SEQ IDNO:227) for aroC and reverse(5′-AGGTTGTGTCATAAAATTTTCCTCCTTAGGTTGGATCAACAGGCACTACG-3′) (SEQ IDNO:228) for pheA,(5′-CAGGGATTCCATTATATATACCTCCTTAACAATTGATCGTCTGTGCCAGG-3′) (SEQ IDNO:229) for aroL,(5′-GTTTCCAGCCATAATTAATTCCTCCTTAGGCTGCCTGGCTAATCCGCGCC-3′) (SEQ IDNO:230) for aroA, and (5′-ACATGCATGCTTACCAGCGTGGAATATCAGTCTTC-3′) (SEQID NO:231) for aroC primers, 1 U Phusion High Fidelity DNA polymerase(NEB), and 50 ng Escherichia coli BL21(DE3) genome in 50 μl,respectively. The amplified DNA fragments were gel purified and elutedinto 30 ul of EB buffer (Qiagen). 5 ul from each DNA solution wascombined and each DNA fragment was spliced by another round of PCR: 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 4 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGACATCGGAAAACCCGTTACTGG-3′) (SEQ ID NO:232)and reverse (5′-ACATGCATGCTTACCAGCGTGGAATATCAGTCTTC-3′) (SEQ ID NO:233)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and SphI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADtyrA-aroLAC.

The DNA fragments encoding pheA, aroL, aroA, and aroC of Escherichiacoli DH10 were amplified by polymerase chain reaction (PCR): 98° C. for10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CCCGAGCTCAGGAGGATATATATATGGTTGCTGAATTGACCGCATTAC-3′) (SEQ IDNO:234) for tyrA,(5′-AATCGCCAGTAAGGAGGAAAATTTTATGACACAACCTCTTTTTCTGATCG-3′) (SEQ IDNO:235) for aroL,(5′-GATCAATTGTTAAGGAGGTATATATAATGGAATCCCTGACGTTACAACCC-3′) (SEQ IDNO:236) for aroA, and(5′-CAGGCAGCCTAAGGAGGAATTAATTATGGCTGGAAACACAATTGGACAAC-3′) (SEQ IDNO:237) for aroC, and reverse(5′-GAGGTTGTGTCATAAAATTTTCCTCCTTACTGGCGATTGTCATTCGCCTG-3′) (SEQ IDNO:238) for tyrA,(5′-CAGGGATTCCATTATATATACCTCCTTAACAATTGATCGTCTGTGCCAGG-3′) (SEQ IDNO:239) for aroL,(5′-GTTTCCAGCCATAATTAATTCCTCCTTAGGCTGCCTGGCTAATCCGCGCC-3′) (SEQ IDNO:240) for aroA, and (5′-ACATGCATGCTTACCAGCGTGGAATATCAGTCTTC-3′) (SEQID NO:241) for aroC, 1 U Phusion High Fidelity DNA polymerase (NEB), and50 ng Escherichia coli BL21(DE3) genome in 50 μl, respectively. Theamplified DNA fragments were gel purified and eluted into 30 ul of EBbuffer (Qiagen). 5 ul from each DNA solution was combined and each DNAfragment was spliced by another round of PCR: 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 4 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGGTTGCTGAATTGACCGCATTAC-3′) (SEQ ID NO:242)and reverse (5′-ACATGCATGCTTACCAGCGTGGAATATCAGTCTTC-3′) (SEQ ID NO:243)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and SphI and ligated into pBAD33pre-digested with the same restriction enzymes.

Construction of pBADpheA-aroLAC-aroG-tktA-aroBDE andpBADtyrA-aroLAC-aroG-tktA-aroBDE.

A DNA fragment 1 (for pheA) and 2 (for tyrA) encoding chloramphenicolacetyltransferase (CAT), P15 origin of replication, araBAD promoter,pheA or tyrA, aroL, aroA, aroC of Escherichia coli DH10B and a DNAfragment 3 encoding araBAD promoter, aroG, tktA, aroB, aroD, and aroE ofEscherichia coli DH10B were amplified separately by polymerase chainreaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 4min, repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward(5′-AAGGAAAAAAGCGGCCGCCCCTGAACCGACGACCGGGTCG-3′) (SEQ ID NO:244) forfragment 1 and 2 and (5′-GCTCTAGAACTTTTCATACTCCCGCCATTCAG-3′) (SEQ IDNO:245) for fragment 3, and reverse(5′-GCTCTAGAGCGGATACATATTTGAATGTATTTAG-3′) (SEQ ID NO:246) for fragment1 and 2 and (5′-AAGGAAAAAAGCGGCCGCGCGGATACATATTTGAATGTATTTAG-3′) (SEQ IDNO:247) for fragment 3, 1 U Phusion High Fidelity DNA polymerase (NEB),and 50 ng pBADpheA-aroLAC, pBADtyrA-aroLAC, and pBADaroG-tktA-aroBDE in50 μl, respectively. Amplified DNA fragments 1 and 2 were digested withNotI and XbaI and ligated into fragment 3 pre-digested with the samerestriction enzymes.

Construction of pTrcBAL.

A DNA sequence encoding benzaldehyde lyase (bal) of Pseudomonasfluorescens of its codon usage optimized for over-expression in E. coliwas amplified by polymerase chain reaction (PCR): 98° C. for 10 sec, 60°C. for 15 sec, and 72° C. for 1 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CATGCCATGGCTATGATTACTGGTGG-3′) (SEQ ID NO:248) and reverse(5′-CCCCGAGCTCTTACGCGCCGGATTGGAAATACA-3′) (SEQ ID NO:249) primers, 1 UPhusion High Fidelity DNA polymerase (NEB), and 50 ng pETBAL in 50 μl.Amplified DNA fragment was digested with NcoI and SacI and ligated intopTrc99A pre-digested with the same restriction enzymes.

Construction of pTrcAdhE2.

A DNA sequence encoding Co-A linked alcohol/aldehyde dehydrogenase(adhE2) of Clostridium acetobutyricum ATCC824 was amplified bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 1 min, repeated 30 times. The reaction mixture contained1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CATGCCATGGCCAAAGTTACAAATCAAAAAG-3′) (SEQ ID NO:250) and reverse(5′-CGAGCTCTTAAAATGATTTTATATAGATATCC-3′) (SEQ ID NO:251) primers, 1 UPhusion High Fidelity DNA polymerase (NEB), and 50 ng Clostridiumacetobutyricum ATCC824 genome in 50 μl. Amplified DNA fragment wasdigested with NcoI and SacI and ligated into pTrc99A pre-digested withthe same restriction enzymes.

Construction of pTrcAdh2.

A DNA sequence encoding alcohol dehydrogenase (adh2) of Saccharomycescerevisiae was amplified by polymerase chain reaction (PCR): 98° C. for10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CATGCCATGGGTATTCCAGAAACTCAAAAAG-3′) (SEQ ID NO:252) andreverse (5′-CCCGAGCTCTTATTTAGAAGTGTCAACAACG-3′) (SEQ ID NO:253) primers,1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ng genome ofSaccharomyces cerevisiae in 50 μl. Amplified DNA fragment was digestedwith NcoI and SacI and ligated into pTrc99A pre-digested with the samerestriction enzymes.

Construction of pTrcBALD.

A DNA sequence encoding CoA-linked aldehyde dehydrogenase (ald) ofClostridium beijerinckii was amplified by polymerase chain reaction(PCR): 98° C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1 min,repeated 30 times. The reaction mixture contained 1× Phusion buffer(NEB), 2 mM dNTP, 0.5 μM forward (5′-CCCCGAGCTCAGGAGGATATACATATGAATAAAGACACACTAATACC-3′) (SEQ ID NO:254) and reverse(5′-CCCAAGCTTAGCCGGCAAGTACACATCTTC-3′) (SEQ ID NO:255) primers, 1 UPhusion High Fidelity DNA polymerase (NEB), and 50 ng pETBAL in 50 μl.Amplified DNA fragment was digested with SacI and HndIII and ligatedinto pTrcBAL pre-digested with the same restriction enzymes.

Construction of pTrcBALK.

A DNA sequence encoding ketoisovalerate decarboxylase (kivd) ofLactococcus lavtis was amplified by polymerase chain reaction (PCR): 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGTATACAGTAGGAGATTACC-3′) (SEQ ID NO:256)and reverse (5′-GCTCTAGATTATGATTTATTTTGTTCAGCAAAT-3′) (SEQ ID NO:257)primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngpETBAL in 50 μl. Amplified DNA fragment was digested with SacI and XbaIand ligated into pTrcBAL pre-digested with the same restriction enzymes.

Construction of pTrcAdh-Kivd.

A DNA sequence encoding ketoisovalerate decarboxylase (kivd) ofLactococcus lavtis was amplified by polymerase chain reaction (PCR): 98°C. for 10 sec, 60° C. for 15 sec, and 72° C. for 1 min, repeated 30times. The reaction mixture contained 1× Phusion buffer (NEB), 2 mMdNTP, 0.5 μM forward(5′-CCCGAGCTCAGGAGGATATATATATGTATACAGTAGGAGATTACC-3′) (SEQ ID NO:258)and reverse (5′-GCTCTAGATTATGATTTATTTTGTTCAGCAAAT-3′) (SEQ ID NO:259)primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngpETBAL in 50 μl. Amplified DNA fragment was digested with SacI and XbaIand ligated into pTrcAdh2 pre-digested with the same restrictionenzymes.

Construction of pTrcBAL-DDH-2ADH.

To remove internal NcoI site, overlap PCR was carried out. DNA fragmentsencoding front and bottom halves of meso-2,3-butanedioldehydrogenase(ddh) of Klebsiella pneumoniae subsp. pneumoniae MGH 78578 and secondaryalcohol dehydrogenase (2adh) of Pseudomanas fluorescens were amplifiedseparately by polymerase chain reaction (PCR): 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 1 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CGAGCTCAGGAGGATATATATATGAAAAAAGTCGCACTTGTTACCG-3′) (SEQ ID NO:260)for front half of ddh, (5′-GGCCGGCGGCCGCGCGATGGCGGTGAAAGTG-3′) (SEQ IDNO:261) for bottom half of ddh,(5′-AACTAATCTAGAGGAGGATATATATATGAGCATGACGTTTTCCGGCCAGG-3′) (SEQ IDNO:262) for front half of 2adh, and(5′-CCTTGCGGAGGGCTCGATGGATGAGTTCGAC-3′) (SEQ ID NO:263) for bottom halfof 2adh, and reverse (5′-CACTTTCACCGCCATCGCGCGGCCGCCGGCC-3′) (SEQ IDNO:264) for front half of ddh,(5′-GCTCATATATATATCCTCCTCTAGATTAGTTAAACACCATCCCGCCGTCG-3′) (SEQ IDNO:265) for bottom half of ddh, (5′-GTCGAACTCATCCATCGAGCCCTCCGCAAGG-3′)(SEQ ID NO:266) for front half of 2adh, and(5′-CCCAAGCTTAGATCGCGGTGGCCCCGCCGTCG-3′) (SEQ ID NO:267) for bottom halfof 2adh, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngKiebsiella pneumoniae subsp. pneumoniae MGH 78578 for ddh andPseudomanas fluorescens genome for 2adh in 50 μl, respectively. Theamplified DNA fragments were gel purified and eluted into 30 ul of EBbuffer (Qiagen). 5 ul from each DNA solution was combined and each DNAfragment was spliced by another round of PCR: 98° C. for 10 sec, 60° C.for 15 sec, and 72° C. for 2 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CGAGCTCAGGAGGATATATATATGAAAAAAGTCGCACTTGTTACCG-3′) (SEQ ID NO:268)and reverse (5′-CCCAAGCTTAGATCGCGGTGGCCCCGCCGTCG-3′) (SEQ ID NO:269)primers, 1 U Phusion High Fidelity DNA polymerase (NEB). The splicedfragment was digested with SacI and HindIII and ligated into pTrcBALpre-digested with the same restriction enzymes.

Construction of pBBRPduCDEGH.

A DNA sequence encoding propanediol dehydratase medium (pduD) and small(pdue) subunits and propanediol dehydratase reactivation large (pduG)and small (pduH) subunits of Klebsiella pneumoniae subsp. pneumoniae MGH78578 was amplified by polymerase chain reaction (PCR): 98° C. for 10sec, 60° C. for 15 sec, and 72° C. for 2 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-GCTCTAGAGGAGGATTTAAAAATGGAAATTAACGAAACGCTGC-3′) (SEQ IDNO:270) and reverse(5′-TCCCCGCGGTTAAGCATGGCGATCCCGAAATGGAATCCCTTTGAC-3′) (SEQ ID NO:271)primers, 1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ngKlebsiella pneumoniae subsp. pneumoniae MGH 78578 in 50 μl. AmplifiedDNA fragment was digested with SacII and XbaI and ligated into pTrc99Apre-digested with the same restriction enzymes to form pBBRPduDEGH.

A DNA sequence encoding propanediol dehydratase large subunit (pduC) ofKlebsiella pneumoniae subsp. pneumoniae MGH 78578 was amplified bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 1 min, repeated 30 times. The reaction mixture contained1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forward(5′-CCGCTCGAGGAGGATATATATATGAGATCGAAAAGATTTGAAGC-3′) (SEQ ID NO:272) andreverse (5′-GCTCTAGATTAGCCAAGTTCATTGGGATCG-3′) (SEQ ID NO:273) primers,1 U Phusion High Fidelity DNA polymerase (NEB), and 50 ng Kiebsiellapneumoniae subsp. pneumoniae MGH 78578 in 50 μl. Amplified DNA fragmentwas digested with XhoI and XbaI and ligated into pBBRPduDEGHpre-digested with the same restriction enzymes.

Construction of pTrcIpdc-Par.

A DNA sequence encoding indole-3-pyruvate (ipdc) of Azospirillumbrasilense and phenylethanol reductase (par) of Rhodococcus sp. ST-10were amplified by polymerase chain reaction (PCR): 98° C. for 10 sec,60° C. for 15 sec, and 72° C. for 1 min, repeated 30 times. The reactionmixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μM forwardprimers (5′-CATGCCATGGGACTGGCTGAGGCACTGCTGC-3′ (SEQ ID NO:314) for ipdcand 5′-CGAGCTCAGGAGGATATATATATGAAAGCTATCCAGTACACCCGTAT-3′ (SEQ IDNO:315) for par, and reverse primers(5′-CGAGCTCTTATTCGCGCGGTGCCGCGTGCAGG-3′ (SEQ ID NO:316) for ipdc and5′-GCTCTAGATTACAGGCCCGGAACCACAACGGCGC-3′ (SEQ ID NO:317) for par, 1 UPhusion High Fidelity DNA polymerase (NEB), and 50 ng pTrcIpdc andpTrcPar, respectively, in 50 μl. Amplified DNA fragment of ipdc and parwere digested with NcoI/SacI and SacI/XbaI, respectively, and wereligated into pTrc99A pre-digested with NcoI and XbaI.

Testing and Results:

To test the butyraldehyde biosynthesis pathway, DH10B harboringpBADButP-atoB/pTrcBALD and pBADButP-atoB-ALD/pTrcB2DH/pBBRpduCDEGH weregrown overnight in LB media containing 50 ug/ml chroramphenicol (Cm⁵⁰)and 100 ug/ml ampicillin (Amp¹⁰⁰) at 37 C, 200 rpm. An aliquot of eachseed culture was inoculated into fresh TB media containing Cm⁵⁰ andAmp¹⁰⁰ and was grown in incubation shaker at 37 C, 200 rpm. Three hoursafter inoculation, the cultures were induced with 13.3 mM arabinose and1 mM IPTG and were grown for overnight. 700 ul of this culture wasextracted with equal volume of ethylacetate and analyzed by GC-MS.

To test the isobutyeraldehyde biosynthesis pathway, DH10B cellsharboring pBADals-ilvCD/pTrcBALK or pBADalsS-ilvCD/pTrcBALK were grownovernight in LB media containing 50 ug/ml chroramphenicol (Cm⁵⁰) and 100ug/ml ampicillin (Amp¹⁰⁰) at 37 C, 200 rpm. An aliquot of each seedculture was inoculated into fresh TB media containing Cm⁵⁰ and Amp¹⁰⁰and was grown in incubation shaker at 37 C, 200 rpm. Three hours afterinoculation, the cultures were induced with 13.3 mM arabinose and 1 mMIPTG and were grown for overnight. 700 ul of this culture was extractedwith equal volume of ethylacetate and analyzed by GC-MS for theproduction of isobutyraldehyde. FIG. 8B shows the production ofisobutanal from these cultures.

To test the 3-methylbutyraldehyde and 2-methylbutyraldehyde biosynthesispathways, DH10B harboring pBADals-ilvCD-LeuABCD/pTrcBALK,pBADals-ilvCD-LeuABCD2/pTrcBALK, pBADals-ilvCD-LeuABCD/pTrcBALK4,pBADalsS-LeuABCD/pTrcBALK, pBADalsS-LeuABCD2/pTrcBALK, orpBADalsS-LeuABCD4/pTrcBALK were grown overnight in LB media containing50 ug/ml chroramphenicol (Cm⁵⁰) and 100 ug/ml ampicillin (Amp¹⁰⁰) at 37C, 200 rpm. An aliquot of each seed culture was inoculated into fresh TBmedia containing Cm⁵⁰ and Amp¹⁰⁰ and was grown in incubation shaker at37 C, 200 rpm. Three hours after inoculation, the cultures were inducedwith 13.3 mM arabinose and 1 mM IPTG and were grown for overnight. 700ul of this culture was extracted with equal volume of ethylacetate andanalyzed by GC-MS. The production of 2-isovaleralcohol (2-methylpental)and 3-isovaleralcohol (3-methylpentanal) was monitored because3-isovaleraldehyde and 2-isovaleraldehyde are spontaneously converted totheir corresponding alcohols. FIG. 8B shows the production of2-methylpental and 3-methylpentanal from these cultures.

To test the phenylacetoaldehyde and 4-hydroxyphenylacetoaldehydebiosynthesis pathways, DH10B cells harboring pBADpheA-aroLAC/pTrcBALK,pBADtyrA-aroLAC/pTrcBALK, pBADaroG-tktA-aroBDE/pTrcBALK,pBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcBALK, andpBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcBALK were grown overnight in LBmedia containing 50 ug/ml chroramphenicol (Cm⁵⁰) and 100 ug/mlampicillin (Amp¹⁰⁰) at 37 C, 200 rpm. An aliquot of each seed culturewas inoculated into fresh TB media containing Cm⁵⁰ and Amp¹⁰⁰ and wasgrown in incubation shaker at 37 C, 200 rpm. Three hours afterinoculation, the cultures were induced with 13.3 mM arabinose and 1 mMIPTG and were grown for overnight. 700 ul of this culture was extractedwith equal volume of ethylacetate and analyzed by GC-MS. The productionof phenylacetoaldehyde, 4-hydroxyphenylaldehyde and their correspondingalcohols were monitored using GC-MS. FIG. 9B shows the production of4-hydroxyphenylethanol from these cultures.

To test the 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol, and2-(indole-3) ethanol biosynthesis pathways, DH10B harboringpBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcBALK,pBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcBALK,pBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcAdh2-Kivd,pBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcAdh2-Kivd,pBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcIpdc-Par, andpBADpheA-aroLAC-aroG-tktA-aroBDE/pTrcIpdc-Par were grown overnight in LBmedia containing 50 ug/ml chroramphenicol (Cm⁵⁰) and 100 ug/mlampicillin (Amp¹⁰⁰) at 37 C, 200 rpm. An aliquot of each seed culturewas inoculated into fresh TB media containing Cm⁵⁰ and Amp¹⁰⁰ and wasgrown in incubation shaker at 37 C, 200 rpm. Three hours afterinoculation, the cultures were induced with 13.3 mM arabinose and 1 mMIPTG and were grown for overnight to a week. 700 ul of this culture wasextracted with equal volume of ethylacetate and analyzed by GC-MS. Theresults are detailed below.

The production of 2-phenylethanol, 2-(4-hydroxyphenyl)ethanol and/or2-(indole-3-)ethanol was monitored using GC-MS. FIG. 42A shows theproduction of 2-phenylethanol from these cultures at 24 hours. FIG. 42Bshows the production of 2-(4-hydroxyphenyl)ethanol from these culturesat 24 hours. FIG. 42C shows the production of 2-(indole-3-)ethanol fromthese cultures at 24 hours.

FIG. 43A shows the GC-MS chromatogram for control (pBAD33 and pTrc99A)at one week. FIG. 43B shows the GC-MS chromatogram for 2-phenylethanol(5.97 min) production from pBADpheA-aroLAC-aroG-tktA-aroBDE and pTrcBALKat one week. FIG. 44 shows the GC-MS chromatogram for2-(4-hydroxyphenyl)ethanol (9.36 min) and 2-(indole-3) ethanol (10.32min) production from pBADtyrA-aroLAC-aroG-tktA-aroBDE and pTrcBALK atone week.

Example 5 Isolation and Biological Activity of Diol Dehydrogenases

Available substrates such as 3-hydroxy-2-butanone (acetoin),4-hydroxy-3-hexanone (propioin), 5-hydroxy-4-octanone (butyroin),6-hydroxy-5-decanone (valeroin), and 1,2-cyclopentanediol were used tomeasure the ability of diol dehydrogenases (ddh) to catalyze thereduction of large saturated α-hydroxyketones to produce a diol. Allreagents were purchased from Sigma-Aldrich Co. and TCI America, unlessotherwise stated.

For cloning and isolation of DDH polypeptides, genomic DNA from severalspecies of bacteria were obtained from ATCC (Lactobaccilus brevis ATCC367, Pseudomanas putida KT2440, and Kiebsiella pneumoniae MGH78578),PCR-amplified (using Phusion with polymerase with 1× Phusion buffer, 0.2mM dNTP, 0.5 μL Phusion enzyme, 1.5 μM primers, and 20 pg template DNAin a 50 μL reaction) utilizing the following protocol: 30 cylces, 98°C./10 secs (denaturing), 60° C./15 secs (annealing), 72° C./30 secs(elongation). Polymerase chain reaction products were then digestedusing restriction enzymes NdeI and BamHI, then ligated into NdeI/BamHIdigested pET28 vectors. Vectors containing ddh clones were transformedinto BL21(DE3) competent cells for protein expression. Single colony wasinnoculated into LB media, and expression of 6×His-tagged proteins ofinterest was induced at OD₆₀₀=0.6 with 0.1 mM IPTG. Expression wasallowed to proceed for 15 hours at 22° C. The 6×His-tagged enzymes werepurified using Ni-NTA spin columns following suggested protocols byQIAGEN, yelding purified protein concentrations in the range of 1.1-6.5mg/mL (determined by Bradford assay).

Diol dehydrogenase ddh 1 was isolated from Lactobaccilus brevis ATCC367, diol dehydrogenase ddh2 was isolated from Pseudomonas putidaKT2440, and diol dehydrogenase ddh3 was isolated from Klebsiellapneumoniae MGH78578. The nucleotide sequence encoding and polypeptidesequence of ddh 1 are shown in SEQ ID NOS:97 and 98, respectively;nucleotide sequence encoding and polypeptide sequence of ddh2 are shownin SEQ ID NOS:99 and 100, respectively; and nucleotide sequence encodingand polypeptide sequence of ddh3 are shown in SEQ ID NOS: 101 and 102,respectively.

Reactions to measure biological activity of DDH polypeptides wereperformed in a final volume of 200 μL as follows: 25 mM substrate, 0.04mg/mL DDH polypeptide, 0.25 mg/mL nicotinamide cofactor, 200 mMimidazole, 14 mM Tris-HCl, and 1.5% by volume DMSO. Biological activitywas assayed using a Molecular Devices Thermomax 96 well plate reader,monitoring absorbance at 340 nm, which corresponds to NADH or NADPHconcentration. For the kinetic studies, 0.04 mg/mL DDH polypeptide, 0.25mg/mL NADH, 20 mM Tris HCl Buffer pH 6.5(red) or 9.0(ox), T=25 C, 100 uLtotal volume was used.

FIG. 12A shows the biological activity of ddh1, ddh2, and ddh3 usingbutyroin as a substrate (triangles represent ddh3 activity). FIG. 12Bshows the oxidation activity of ddh3 towards 1,2-cyclopentanediol and1,2-cyclohexanediol as measured by NADH production. FIG. 13 summarizesthe results of kinetic studies for various substrates in the oxidationreactions catalyzed by the DDH polypeptides. These reactions were NAD+dependent.

Example 6 Sequential In Vivo Biological Activity of CC-Ligases (Lyases)and Diol Dehydrogenases

The ability of a C—C lyase and a diol hydrogenase to perform thefollowing sequential reaction was tested in E. coli:

For α-hydroxyketone and diol production, a pathway comprising abenzaldehyde lyase (bal) gene isolated from Pseudomonas fluorescens(codon usage was optimized for E. coli protein expression) andmeso-2,3-butanediol dehydrogenase (ddh) gene isolated from Kiebsiellapneumoniae subsp. pneumoniae MGH 78578 was constructed in E. coli andtested for its ability to condensate the substrates detailed below inTable 2 (e.g., acetoaldehyde, propionaldehyde, butyraldehyde,isobutyraldehyde, 2-methyl-butyraldehyde, 3-methyl-butyraldehyde,phenylacetaldehyde, and 4-hydroxyphenylacetaldehyde, or theircorresponding alcohols) to form α-hydroxyketone and the correspondingdiol in vivo. The production of various α-hydroxyketones and diols wasmonitored by gas chromatography-mass spectrometry (GC-MS).

TABLE 2 Summary of substrates and products. Produced Substrateα-hydroxyketone Produced diol FIGS. Butanal 5-Hydroxy-4-octanone4,5-Octanonediol 17A & B n-Pentanal 6-Hydroxy-5-decanone 5,6-Decanediol18A & B 3-Methylbutanal 2,7-Dimethyl-5-hydroxy-4-2,7-Dimethyl-4,5-octanediol 19A & B octanone n-Hexanal7-Hydroxy-6-dodecanone 6,7-dodecanediol 20A & B 4-Methylpentanal2,9-Dimethyl-6-hydroxy-5- 2,9-Dimethyl-5,6-decanediol 21A & B decanonen-Octanal 9-Hydroxy-8-hexadecanone 8,9-hexadecanediol 22 Acetaldehyde3-Hydroxy-2-butanone 2,3-Butanediol 23 n-Propanal 4-Hydroxy-3-hexanone3,4-Hexanediol 24A & B Phenylacetoaldehyde 1,4-Diphenyl-3-hydroxy-2-1,4-Diphenyl-2,3-butanediol 25 butanone

For Analysis of ≦C10.

E. coli harboring pTrcBAL-DDH-2ADH was grown for overnight in LB mediacontaining 50 ug/ml Kanamycine (Km). This seed culture was innoculatedinto M9 media containing 3% (v/v) glycerol, 0.5% (g/v) and 50 ug/ml Km.10 mL cultures were grown to O.D.₆₀₀=0.7, then cultures were inducedwith 0.5 mM IPTG. The cells were allowed to express the enzymes ofinterest for 3 hours before various aldehydes were added to aconcentration of 5-10 mM. After addition of aldehydes, the cultures werecapped and incubated at 37° C. with shaking for 72 hours. Cultures wereextracted with 2 mL ethyl acetate, and analyzed on GC-MS using thefollowing protocol:

1 μL injection w/50:1 split

Inlet temperature—150° C.

Initial oven temperature—50° C.

Temperature Ramp 1—10° C./min to 150° C.

Temperature Ramp 2—50° C./min to 300° C.

GC to MS transfer temp—250° C.

MS detection—full scan MW 35-200

For Analysis of ≧C12.

E. coli DH10B strains harboring pTrc99A (Ctrl vector) or pTrcBAL wereinoculated into 0.75×M9/0.5% LB containing 0.1 mM CaCl₂, 2 mM MgSO₄, 1mM KCl, 1% galacturonate, 5 μg/mL thiamine, Amp. The cultures were grownup to an optical density (600 n nm) of 0.8 and induced with 0.25 mMIPTG. The cells were allowed to express the proteins for 2.5 hours at37° C., then aldehyde substrate was added to a concentration of 5 mM,the culture vial was capped tightly and incubated for 72 hours at 37° C.w/shaking 200 rpm. 1 mL of the final culture was extracted with 0.75 mLof ethyl acetate, centrifuged facilitate phase separation, then analyzedvia GCMS using the following method.

1 μL injection w/50:1 split

Inlet temperature—250° C.

Initial oven temperature—50° C.

Temperature Ramp 1—10° C./min to 125° C.

Temperature Ramp 2—30° C./min to 300° C.

Final Temperature 300° C.—1 minute

GC to MS transfer temp—250° C.

MS detection—full scan MW 40-260.

The results are depicted in FIGS. 17 through 25. FIG. 17 shows thesequential conversion of butanal into 5-hydroxy-4-octanone and then4,5-octanonediol. FIG. 18 shows the sequential conversion of n-pentanalinto 6-hydroxy-5-decanone and then 5,6-decanediol. FIG. 19 shows theconversion of 3-methylbutanal into 2,7-dimethyl-5-hydroxy-4-octanone andthen 2,7-Dimethyl-4,5-octanediol. FIG. 20 shows the sequentialconversion of n-hexanal into 7-hydroxy-6-dodecanone and then6,7-dodecanediol. FIG. 21 shows the conversion of 4-methylpentanal into2,9-dimethyl-6-hydroxy-5-decanone and then 2,9-dimethyl-5,6-decanediol.FIG. 22 shows the conversion of n-octanal into 9-hydroxy-8-hexadecanone.FIG. 23 shows the conversion of acetaldehyde into 3-hydroxy-2-butanone.FIG. 24 shows the sequential conversion of n-propanal into4-hydroxy-3-hexanone and then 3,4-hexanediol. FIG. 25 shows theconversion of phenylacetoaldehyde into1,4-diphenyl-3-hydroxy-2-butanone.

Similar to above, a pathway comprising a benzaldehyde lyase (bal) geneisolated from Pseudomonas fluorescens (codon usage was optimized for E.coli protein expression) was constructed in E. coli and tested for itsability to catalyze the production of various α-hydroxyketones. Theresults, which show the broad spectrum of C—C ligase activity for thebal gene tested, are set forth in FIG. 48 through FIG. 55.

Example 7 Sequential Biological Activity of Diol Dehydrogenases and DiolDehydratases

To test the sequential biological activity of diol dehydrogenases anddiol dehydratases in a dehydration and reduction pathway, butyroin wasused as a substrate in a sequential reaction to produce 4-octanone. Theenzyme diol dehydrogenase (e.g., ddh) catalyzes the reversible reductionand oxidation of α-hydroxy ketones and its corresponding diol, such as5-hydroxy-4-octanone and 4,5-octanediol, and the enzyme diol dehydratase(e.g., pduCDE) catalyzes the irreversible dehydration of diols, such as4,5-octanediol.

Diol dehydrogenase ddh from Kiebsiella pneumoniae MGH 78578 and dioldehydratase pduCDE from Kiebsiella pneumoniae MGH 78578 were cloned intoa bacterial expression vector and expressed and purified on a Ni-NTAcolumn, as described in Example X except that 1 mM of 1,2-propanediolwas added at all time during the expression and purification of dioldehydratase. The large, medium, and small subunits of the pduCDEpolyeptide are encoded by the nucleotide sequences of SEQ ID NOs:103,105, and 107, respectively, and the polypeptide sequence are set forthin SEQ ID NOs: 104, 106, and 108, respectively.

The ddh3 and pduCDE polypeptides were incubated with butyroin and theirappropriate cofactors, then assayed using gas chromatography-massspectrometry (GC-MS) for their ability to perform sequential reactionsresulting in the product 4-octanone. Reaction conditions are given inTable 3 below. The reaction mixture was incubated at 37° C. for 40 hoursin a 0.6 mL eppendorf tube with minimal head space. The reaction productwas extracted with an equivalent volume of ethyl acetate, stored in aglass vial, and sent to Thermo Fischer Scientific Instruments Divisionfor compositional analysis by GC-MS.

TABLE 3 Reaction Conditions Rxn Component Concentration5-hydroxy-4-octanone (butyroin)  8.4 mM Adenosylcobalamin (coenzyme B₁₂)33.5 μM KCl  9.6 mM NADH   18 mM dDH3 enzyme 0.19 mg/mL dDOH1 enzyme mix0.15 mg/mL Reaction Buffer   10 mM Tris HCl pH 7.0

FIG. 26A shows GC-MS data which confirms the presence of 4,5-octanediolin the sample extraction. The mass-spectra of the peaks, retention time,at 5.36 was identified as butyroin (substrate), and at 6.01, 6.09, and6.12 min were identified as different isomers of 4,5-octanediol. Thiscompound is the expected product resulting from the reduction ofbutyroin by ddh3.

FIG. 26B shows GC-MS data confirming the presence of 4-octanone in thesample extraction. The mass-spectra of the peak, retention time, at 4.55was identified as 4-octanone. This compound is the expected productresulting from the sequential dehydrogenation of butyroin anddehydration of 4,5-octanediol by ddh3 and pduCDE, respectively.

FIGS. 27A and 27B show comparisons between the sample extraction gaschromatograph/mass spectrum and the 4-octanone standard gaschromatograph/mass spectrum. These results demonstrate that 4-octanonewas produced from butyroin using the enzymes diol dehydrogenase (ddh3)and a diol dehydratase (pduCDE). GC-MS analysis of the incubatedreaction mixture confirmed starting material, intermediate and product,demonstrating that these enzymes can be reappropriated for thesespecific substrates.

Example 8 Isolation and Biological Activity of Secondary AlcoholDehydrogenases

Substrates such as 4-octanone, 2,7-dimethyl-4-octanone, cyclopentanoneand corresponding alcohols were utilized to measure the ability ofsecondary alcohol dehydrogenases (2ADHs) to catalyze the reduction oflarge saturated ketones to secondary alcohols. An example of a reactioncatalyzed by secondary alcohol dehydrogenases is illustrated below(reduction of 4-octanone to 4-octanol is shown):

All enzymes and reagents were purchased from New England Biolabs andSigma, respectively, unless otherwise stated.

Various secondary alcohol dehydrogenases (2ADHs) were isolated fromPseudomonas putida KT2440, Pseudomonas fluorescens Pf-5, and Kiebsiellapneumoniae MGH 78578. All vectors were transformed in BL21(DE3)competent cells and expression of the genes encoding the proteins ofinterest was induced with IPTG (via the T7 promoter). The cells werelysed, proteins were extracted and then purified on Ni-NTA columns.Final protein concentration in the Ni-NTA eluate was diluted to 0.15mg/mL prior to assays.

NADPH/NADPH consumption and production assays were performed using aTHERMOmax microplate reader in the kinetic mode, monitoring the NADPHabsorbance peak at 340 nm until the reaction reached equilibrium. In theassay described in Table 2, 2ADH-2, 2ADH-5, 2ADH-8, and 2ADH-10 weretested for their ability to either catalyze the oxidation of 4-octanolor catalyze the reduction of 4-octanone. These reaction conditions arefound in Table 4 below.

TABLE 4 Reaction Conditions for Various Enzyme Assays Reaction ComponentFinal Concentration NADH Production Assay (30° C.) 2ADH enzyme Approx.0.058 μg/μL 4-octanol 5.55 mM NAD+ Approx. 1.4 μg/μL Imidizole (fromElution Buffer) Approx. 280 mM NADH Consumption Assay (30° C.) 2ADHenzyme Approx. 0.075 μg/μL 4-octanone 5.0 mM NADH Approx. 0.25 μg/μLImidizole (from Elution Buffer) Approx. 250 mM NADPH Production Assay(30° C.) 2ADH enzyme Approx. 0.058 μg/μL 4-octanol 5.55 mM NADP+ Approx.1.4 μg/μL Imidizole (from Elution Buffer) Approx. 280 mM

Further testing was performed, as described in Tables 5 below, in which2ADH-2, 2ADH-11, 2ADH-12, 2ADH-13, 2ADH-14, 2ADH-15, 2ADH-16, 2ADH-17,and 2ADH-18 were tested for their ability to either catalyze theoxidation of 4-octanol, 2,7-dimethyl-4-octanonol, or cyclopentanol, orcatalyze the reduction of 4-octanone, 2,7-dimethyl-4-octanonone, orcyclopentanone.

TABLE 5 Rxn Component Final Concentration Rxn Components for NADPHConsumption Assays (Reduction) Substrate 25 mM Enzyme 0.04 mg/mLNicotinamide cofactor 0.25 mg/mL Imidizole 200 mM Tris HCl 14 mM DMSO1.5% by volume Total Volume 200 μL Rxn Components for NAD(P)H ProductionAssays (Oxidation) Substrate 5 mM Enzyme 0.04 mg/mL Nicotinamidecofactor 0.25 mg/mL Imidizole 200 mM Tris HCl 14 mM Rxn Components forNAD(P)H Production Assay using 2,7-dimethyl-4- octanone as a substrateSubstrate 50 mM Enzyme 0.08 mg/mL Nicotinamide cofactor 0.25 mg/mLImidizole 200 mM Tris HCl 14 mM DMSO 3% by volume

FIG. 30A shows the results from the NADH Production Assay of Table 3, inwhich 2ADH-2 catalyzes the oxidation of 4-octanol in the presence ofNAD+, as measured by NADH production. FIG. 30B shows the results of theNADPH Production Assay of Table 3, in which 2ADH-5, 2ADH-8, and 2ADH-10catalyze the oxidation of 4-octanol in the presence of NADP+, asmeasured by NADPH production.

FIG. 31 shows the oxidation of 4-octanol by 2ADH-11 (FIG. 31A) and2ADH-16 (FIG. 31B), as measured by NADH and NADPH production,respectively. FIG. 32 shows the oxidation of 2,7-dimethyloctanol by2ADH-11 and others (FIG. 32A) and 2ADH-16 (FIG. 32B), as measured byNADH and NADPH production, respectively.

FIG. 33A shows the reduction of 2,7-dimethyl octanol by 2ADH 11 and2ADH16 as monitored by NADPH consumption. FIG. 33B shows the reductionactivity of both 2ADH11 and 2ADH16 towards various substrates. FIG. 34shows the oxidation (FIG. 34A) and reduction (FIG. 34B) of cyclopentanolby 2ADH-16.

Similar to above, kinetic testing for both oxidation and reductionreactions was performed on various substrates using 2ADH-16. Theconditions for these studies were as follows: 0.04 mg/mL enzyme, 0.25mg/mL cofactor, 20 mM Tris HCl Buffer pH 6.5(red) or 9.0(ox), T=25 C,100 uL total volume was used. The calculated rate constants for thereduction reactions, along with the structures of the substrates, aresummarized in FIG. 35. The calculated rate constants for the oxidationreactions, along with the structures of the substrates, are summarizedin FIG. 36. These results show that 2ADH-16 is capable of catalyzingboth the oxidation and reduction of a wide variety of substrates.

Example 9 Isolation and In Vitro and In Vivo Activity of Coenzyme B 12Independent Diol Dehydratases

Substrates such as 1,2-propanediol, meso-2,3-butanediol, andtrans-1,2-cyclopentanediol were utilized to test both the in vitro andin vivo biological activity of a B12 independent diol dehydratase in adehydration and reduction pathway. Diol dehydratases catalyzes theirreversible dehydration of diols, such as 1,2-propanediol.

For in vitro activity, E. coli BL21(DE3) harboring pETPduCDE (dioldehydratase subunits) was inoculated into 100 mL LB media, grown toOD₆₀₀=0.7, induced with 0.15 mM IPTG, and incubated for 22 hours at 22°C. The cells were lysed and proteins of interest were purified on aNi-NTA spin column. Purification of all three dehydratase subunits wasaccomplished by adding 5 mM 1,2-propanediol to the lysis and washbuffers. The Ni-NTA purification yielded approximately 660 μL of proteinmixture at a concentration of 2.2 mg/mL. Protein concentration assayswere conducted using a Bradford reagent protocol.

The purified PduCDE was used to set up in vitro diol dehydratasereactions. Three assays were conducted with 1,2-propanediol andmeso-2,3-butanediol. Control reactions were also set up with elutionbuffer added in place of purifiedPduCDE. In vitro reactions wereconducted under semi-anaerobic conditions in 2 mL screw cap glass vials.Reaction components and concentrations are given in Table 6.

TABLE 6 Reaction conditions for B₁₂ dependent DDOH in vitro assay RxnComponent Concentration Diol substrate 10 mM Adenosylcobalamin (B₁₂) 100μg/mL KCl 10 mM dOH1 enzyme mix 0.08 mg/mL Reaction Buffer 10 mM TrisHCl pH 7.5

After 48 hours, 1 mL of the reaction mixture was extracted with 0.5 mLof either ethylacetate or hexanol and analyzed by GCMS.

The following GCMS protocol was used for all experiments:

1 μL injection w/50:1 split

Inlet temperature—250° C.

Initial oven temperature—50° C.

Temperature Ramp 1—10° C./min to 125° C.

Temperature Ramp 2—30° C./min to 300° C.

Final Temperature 300° C.—1 minute

GC to MS transfer temp—250° C.

MS detection—full scan MW 40-260

The results are shown in FIG. 45. FIG. 45A confirms the formation of1-propanal from 1,2-propanediol, and FIG. 45B confirms the formation of2-butanone from meso-2,3-butanediol, both of which were catalyzed by B12independent diol dehydratase.

For in vivo activity, the pBBRDhaB1/2 plasmid was constructed asfollows: the DNA sequence encoding B12-independent glycerol dehydratase(dhaB1) and activator (dhaB2) of Clostridium butyricum was amplified bypolymerase chain reaction (PCR): 98° C. for 10 sec, 60° C. for 15 sec,and 72° C. for 2 min for dhaB1 and 1 min for dhaB2, repeated 30 times.The reaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5μM forward primers (5′-CCGCTCGAGGAGGATATATATATGATTTCTAAAGGCTTTAGCACCC-3′(SEQ ID NO:318) for dhaB1 and5′-ACGTGATGTAATCTAGAGGAGGATATATATATGAGCAAAGAAATTAAAGG-3′ (SEQ ID NO:319)for dhaB2, and reverse primers(5′-TCTTTGCTCATATATATATCCTCCTCTAGATTACATCACGTGTTCAGTAC-3′ (SEQ IDNO:320) for dhaB1 and 5′-CGAGCTCTTATTCGGCGCCAATGGTGCACGGG-3′ (SEQ IDNO:321) for dhaB2, 1 U Phusion High Fidelity DNA polymerase (NEB), and50 ng pETdhaB1 and pETdhaB2, respectively, in 50 μl. Amplified fragmentswere gel purified and spliced by another round of PCR: 98° C. for 10sec, 60° C. for 15 sec, and 72° C. for 2.5 min, repeated 30 times. Thereaction mixture contained 1× Phusion buffer (NEB), 2 mM dNTP, 0.5 μMforward (5′-CCGCTCGAGGAGGATATATATATGATTTCTAAAGGCTTTAGCACCC-3′) (SEQ IDNO:322) and reverse primers (5′-CGAGCTCTTATTCGGCGCCAATGGTGCACGGG-3′)(SEQ ID NO:323), 1 U Phusion High Fidelity DNA polymerase (NEB), and 50ng each fragment in 50 μl. Amplified DNA fragment was digested with XhoIand SacI and ligated into pBBR1MCS-2 pre-digested with the samerestriction enzymes.

Two strains of E. coli DH10B harboring pBBR1MCS-2 or pBBRDhaB1/2 into TBmedia without glycerol were innoculated. Cultures were grown toOD₆₀₀=0.5 and the substrates 1,2-propanediol, meso-2,3-butanediol, andtrans-1,2-cyclopentanediol were added to separate cultures to aconcentration of 10 mM. 5 ug/ml of co-enzyme S-adenosylmethionine wasadded before the culture is transferred to anaerobic environment. Thecultures were incubated at 37 C for 48 hrs.

After 48 hours, 1 mL of culture was extracted with 0.5 mL ofethylacetate or hexanol and analyzed by GCMS, as described above. Theresults are shown in FIG. 46. FIG. 46A shows the in vivo production of1-propanol from 1,2-propanediol. FIG. 46B shows the in vivo productionof 2-butanol from meso-2,3 butanediol. FIG. 46C shows the in vivoproduction of cyclopentanone from trans-1,2-cyclopentanediol.

Example 10 Identification of Secreted Alginate Lyase and Genomic RegionsSufficient for Growth on Alginate as a Sole Source of Carbon

To identify secreted or external alginate lyases, and to identifygenomic regions from Vibrio splendidus that are sufficient to confergrowth in alginate as a sole source of carbon, the following clones weremade using the gateway system from Invitrogen (Carlsbad, Calif.). First,entry vectors were made by TOPO cloning PCR fragments into pENTR/D/TOPO.PCR fragments were generated using Vibrio splendidus B01 genomic DNA asa template and amplified with the following primer pairs:

Vs24214-24249: genomic region corresponding to gene id betweenV12B01_(—)24214 and V12B01_(—)24249 (see Example 1).

TABLE 7 24214 F cacc caagcgatagtttatatagcgt (SEQ ID NO: 324) 24249 Rgaaatgaacggatattacgt (SEQ ID NO: 325)

Vs24189-24209; genomic region corresponding lo gene id betweenV12B01_(—)24189 and V12B01_(—)24209 (see Example 1).

TABLE 8 24189 R cggaacaggtgattgtggt (SEQ ID NO: 326) 24209 F cacc (SEQ ID NO: 327) gcccacttcaagatgaagctgt

Vs24214-24239; genomic region corresponding to gene id betweenV12B01_(—)24214 and V12B01_(—)24239 (see Example 1).

TABLE 9 24214 F cacc  (SEQ ID NO: 328) caagcgatagtttatatagcgt 24239 R_1gtggctaagtacatgccggt (SEQ ID NO: 329)

The entry vectors were recombined with the destination vector pET-DEST42(Invitrogen) using the LR recombinase enzyme (Invitrogen). Thesedestination vectors were then put into electrocompetent DH10B or BL21cells.

The alginate lyase clones were then made by digesting (using enzymes NdeI and Bam HI) the PCR products that were generated using Vibriosplendidus 12B01 genomic DNA as a template and amplified with thefollowing primer pairs:

TABLE 10 24214 ndeF GGAATTC CAT atgacaaagaatatgacgactaaac(SEQ ID NO: 330) for forward primer for V12B01_24214 24214 bamRCG GGATCC ttattatttcccctgccctgcagt (SEQ ID NO: 331)for reverse primer for V12B01_24214 24219 ndeFGGAATTC CAT atgagctatcaaccacttttac (SEQ ID NO: 332)for forward primer for V12B01_24219 24219 bamRCG GGATCC ttacagttgagcaaatgatcc (SEQ ID NO: 333)for reverse primer for V12B01_24219

The digested PCR products were then ligated into cut pET28 vector.Certain of the cloned genomic regions of Vibrio splendidus B01 weretested for the presence of secreted alginate lyases, and theabove-described constructs were tested in various combinations for theability to confer growth on alginate as a sole source of carbon.

The Vs24254 (SEQ ID NO: 32) region of Vibro spendidus encodes afunctional external alginate lyase. BL21 cells expressing Vs24254 fromthe pET28 vector were capable of breaking down alginate in the growthmedium. When grown on LB+2% alginate+0.1 mM Isopropylβ3-D-1-thiogalactopyranoside (IPTG), only cells expressing the Vs24254gene give a positive TBA assay result of pink color. This assay wasperformed by spinning down an overnight culture grown on the abovementioned media. The media was then mixed in a 1:1 ratio with 0.8%thiobarbituric acid (TBA), heated for 10 min at 99 degrees Celsius, andassayed for pink coloration. FIG. 47 shows the results of this assay.The left tube in FIG. 47 represents media taken from an overnightculture of cells expressing Vs24254, while the right hand tube shows theTBA reaction using media from cells expressing Vs24259 (negativecontrol). The lack of pink coloration in the negative control indicatesthat little or no cleavage of the alginate polymer has occurred.Wildtype E. coli cells not expressing any recombinant proteins show thesame coloration as the negative control Vs24259 (data not shown).

To test the ability of recombinant E. coli to grow on alginate as a solesource of carbon, transformed cells were grown for 19 hours at 30degrees Celsius with mild shaking in a 96-well plate. Each well held 222μl of minimal media (see growth conditions for explanation of minimalmedia) with the 0.66% carbon source in the form of either degradedalginate or glucose (positive control for growth). All cells were eitherBL21 with no plasmid (BL21—negative control), one plasmid (Da or 3a), ortwo plasmids (Dk3a and Da3k). The plasmids are indicated by the lowercase letter: “a” refers to the plasmid backbone pET-DEST42 and “k”refers to the pENTR/D/TOPO backbone. “D” indicates that the plasmidcontains the genomic region Vs24214-24249, while “3” indicates that theplasmid contains the genomic region Vs24189-24209. Thus, Da would bepET-DEST42-Vs24214-24249, Da3k would be pET-DEST42-Vs24214-24249 andpENTR/D/TOPO-Vs24189-24209 and so on.

As shown in FIG. 56A, the two vector-constructs pET-DEST42-Vs24214-24249and pENTR/D/TOPO-Vs24189-24209 when combined in E. coli confer growth ondegraded alginate as the sole carbon source. This same result is beobserved when these genomic inserts are switched into the oppositevector (pET-DEST42-Vs24189-24209 and pENTR/D/TOPO-Vs24214-24249). FIG.56B shows growth on glucose as a positive control. Thus, the combinedgenomic regions of Vs24214-24249 and Vs24189-24209 from Vibro splendiduswere sufficient to confer on E. coli the ability to grown on alginate asa sole source of carbon.

Example 11 Production of Ethanol from Alginate

The ability of recombinant E. coli to produce ethanol by growing onalginate on a source of carbon was tested. To generate recombinant E.coli, DNA sequences encoding pyruvate decarboxylase (pdc), and twoalcohol dehydrogenase (adhA and adhB) of Zymomonas mobilis wereamplified by polymerase chain reaction (PCR). These amplified fragmentswere gel purified and spliced together by another round of PCR. Thefinal amplified DNA fragment was digested with BamHI and XbaI ligatedinto pBBR1MCS-2 pre-digested with the same restriction enzymes. Theresulting plasmid is referred to as pBBRPdc-AdhA/B.

E. coli was transformed with either pBBRPdc-AdhA/B or pBBRPdc-AdhA/B+1.5Fos (fosmid clone containing genomic region between VI 2B01_(—)24189 andV12B01_(—)24249; these sequences confer on E. coli the ability to usealginate as a sole source of carbon, see Examples 1 and 10), grown in m9media containing alginate, and tested for the production of ethanol. Theresults are shown in FIG. 57, which demonstrates that the strainharboring pBBRPdc-AdhA/B+1.5 FOS showed significantly higher ethanolproduction when growing on alginate. These results indicate that thepBBRPdc-AdhA/B+1.5 FOS was able to utilize alginate as a source ofcarbon in the production of ethanol.

The various embodiments described above can be combined to providefurther embodiments. All of the U.S. patents, U.S. patent applicationpublications, U.S. patent applications, foreign patents, foreign patentapplications and non-patent publications referred to in thisspecification and/or listed in the Application Data Sheet, areincorporated herein by reference, in their entirety. Aspects of theembodiments can be modified, if necessary to employ concepts of thevarious patents, applications and publications to provide yet furtherembodiments.

These and other changes can be made to the embodiments in light of theabove-detailed description. In general, in the following claims, theterms used should not be construed to limit the claims to the specificembodiments disclosed in the specification and the claims, but should beconstrued to include all possible embodiments along with the full scopeof equivalents to which such claims are entitled. Accordingly, theclaims are not limited by the disclosure.

The following publications are herein incorporated by reference in theirentirety.

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1. A method of producing 2-keto-3-deoxy D-gluconate (KDG), comprising:a) providing 4-deoxy-L-erythro-5-hexoseululose uronic acid (DEHU); b)providing recombinant DEHU hydrogenase wherein said DEHU hydrogenasecomprises SEQ ID NO:92; and c) contacting said DEHU with saidrecombinant DEHU hydrogenase whereby said DEHU is converted to KDG bysaid recombinant DEHU hydrogenase.
 2. The method of claim 1 wherein saidKDG is produced in a microorganism.
 3. The method of claim 2 wherein themicroorganism is yeast.
 4. The method of claim 2 wherein themicroorganism is E. Coli.
 5. The method of claim 2 wherein said KDG isconverted to a commodity chemical in the microorganism.